[go: up one dir, main page]

EP4036238A1 - Functional nucleic acid molecule and method - Google Patents

Functional nucleic acid molecule and method Download PDF

Info

Publication number
EP4036238A1
EP4036238A1 EP21153875.6A EP21153875A EP4036238A1 EP 4036238 A1 EP4036238 A1 EP 4036238A1 EP 21153875 A EP21153875 A EP 21153875A EP 4036238 A1 EP4036238 A1 EP 4036238A1
Authority
EP
European Patent Office
Prior art keywords
enhancer
synthetic super
cell
super
cells
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP21153875.6A
Other languages
German (de)
French (fr)
Inventor
Ute Koeber
Mantas Matjusaitis
Steven Pollard
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of Edinburgh
Original Assignee
University of Edinburgh
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by University of Edinburgh filed Critical University of Edinburgh
Priority to EP21153875.6A priority Critical patent/EP4036238A1/en
Priority to EP22703431.1A priority patent/EP4284935A1/en
Priority to KR1020237029045A priority patent/KR20230137399A/en
Priority to PCT/GB2022/050206 priority patent/WO2022162361A1/en
Priority to CN202280011408.1A priority patent/CN116867901A/en
Priority to JP2023544676A priority patent/JP2024504412A/en
Priority to BR112023014906A priority patent/BR112023014906A2/en
Priority to US18/274,306 priority patent/US20240092847A1/en
Priority to CA3206298A priority patent/CA3206298A1/en
Priority to AU2022212766A priority patent/AU2022212766A1/en
Publication of EP4036238A1 publication Critical patent/EP4036238A1/en
Withdrawn legal-status Critical Current

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1086—Preparation or screening of expression libraries, e.g. reporter assays
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A61K48/0066—Manipulation of the nucleic acid to modify its expression pattern, e.g. enhance its duration of expression, achieved by the presence of particular introns in the delivered nucleic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C07K14/4705—Regulators; Modulating activity stimulating, promoting or activating activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
    • C12N9/1211—Thymidine kinase (2.7.1.21)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/01—Phosphotransferases with an alcohol group as acceptor (2.7.1)
    • C12Y207/01021—Thymidine kinase (2.7.1.21)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/008—Vector systems having a special element relevant for transcription cell type or tissue specific enhancer/promoter combination
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/15—Vector systems having a special element relevant for transcription chimeric enhancer/promoter combination

Definitions

  • the invention relates to synthetic super-enhancers activated by one or more transcription factors.
  • the present invention relates to synthetic super-enhancers that are activated by transcription factors expressed in target cells and are coupled to an adverse payload in order to kill target cells upon activation.
  • the invention also relates to synthetic super-enhancers activated by one or more transcription factors of the SOX family.
  • WO2014066848 and US2014/0296218 describe natural super-enhancers that are claimed to be useful for modulating expression of cell type-specific genes and methods for identifying said super-enhancers.
  • WO2017155973 describes synthetic enhancers for use in recombinant parvoviruses, particularly enhancers with reduced size to enable delivery of large genetic payloads.
  • WO2012101191 describes designing promoters for selective expression of genes by using transcription factor binding site motif prediction to create minimized promoters based on these motifs.
  • a synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
  • a functional nucleic acid molecule comprising the synthetic super-enhancer described herein, operably linked to a transgene.
  • a functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
  • a synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif.
  • a synthetic super-enhancer activated by SOX2 wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif.
  • a vector comprising the synthetic super-enhancer or the functional nucleic acid molecule as described herein.
  • composition comprising the synthetic super-enhancer, the functional nucleic acid molecule or the vector as described herein, and an acceptable carrier.
  • composition comprising the functional nucleic acid molecule described herein, for use in therapy.
  • composition comprising the functional nucleic acid molecule described herein, for use in the treatment of cancer.
  • kits comprising the functional nucleic acid molecule comprising an adverse payload as described herein, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug, and wherein the kit additionally comprises said inactive prodrug for administration with the functional nucleic acid molecule, vector or composition.
  • a method for treating cancer comprising administering the functional nucleic acid molecule or the composition as described herein, to a patient.
  • a method for treating glioblastoma comprising administering a functional nucleic acid molecule and an inactive prodrug to a patient,
  • the present invention relates to novel synthetic super-enhancers (SSEs) and provides an innovative way of delivering transgenes, such as therapeutic and adverse payloads.
  • SSEs synthetic super-enhancers
  • the inventors reasoned it might be possible to create SSEs by artificially assembling enhancers that retain the core functional elements and transcription factor motifs within full length enhancers. Importantly, this includes utilizing the natural and functional flanking sequence surrounding the direct transcription factor motifs in these enhancers.
  • This strategy aims to enable retention of the natural local transcription factor (TF) binding context for the key cell type-specific TFs (low affinity with appropriate spacing), but facilitates high concentrations of TF binding to trigger strong transcription, i.e., capturing the appropriate grammar (spacing, affinity and orientation of co-binding proteins) of the TF motifs within cell type specific enhancers, but boosting transcriptional activity by combining in multi-part arrays.
  • TF natural local transcription factor
  • a synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
  • Enhancer refers to a short region (usually 50-1500 bp) of DNA which is bound by proteins (for example, transcription factors) to enhance transcription of a gene. Enhancers typically act as cis-regulatory elements but may also act in trans, and may activate more than one target gene. Due to DNA folding and conformation or through promotion of multi-molecular compartments (referred to as transcriptional hubs or condensates, which may form by phase separation) they can be located distally from the transcription start site (TSS) of the gene being regulated. In contrast, promoters are upstream of the TSS on the same DNA sequence proximal to the site of transcriptional initiation. Promoters will be bound by RNA polymerase II in order to initiate transcription.
  • proteins for example, transcription factors
  • H3K27Ac is a histone modification commonly found at enhancers and can be used to predict regions of enhancer activity. Determination of whether a sequence enhances gene transcription (and therefore may be referred to as an "enhancer”) can be determined using methods known in the art, most typically using a plasmid based reporter assay.
  • Super-enhancers are also involved in the activation or regulation of transcription.
  • the term "super-enhancer” refers to a sequence that contains clusters of multiple enhancers, usually spanning a region of 5-15kb. These "super-enhancers” are highly occupied by transcriptional coactivators, such as the Mediator complex, compared to the average enhancers. They exhibit greater activity than average enhancers, and are frequently involved in driving expression of cell type-specific genes involved in maintaining cell identity or disease state (see, for example, US2014/0296218 and US2014/0287932 , which are herein incorporated by reference in their entirety).
  • SSE synthetic super-enhancer
  • a super-enhancer not found in nature, i.e. is an artificially constructed super-enhancer designed for the purposes described herein, which may exhibit features associated with natural super-enhancers.
  • an SSE is an artificial construct comprising two or more enhancer sequences.
  • the SSE may be highly enriched for transcription factor motifs to stimulate transcriptional activation. This enables SSE sequences to be shorter than natural super-enhancers because the high concentration of transcription factor binding to the SSE promotes transcriptional activity.
  • the present invention provides an innovative way of delivering a transgene by coupling it to an SSE that is activated by a transcription factor - or unique combination of transcription factors - expressed in a target cell. Therefore, endogenous expression of the transcription factor(s) in the target cell is used to initiate expression of the exogenous transgene in a highly selective manner.
  • the transcription factor has cell type or lineage-specific expression patterns and is therefore minimally expressed in cells other than the target cell, i.e., it is not ubiquitously expressed. This enables cell-type or cell state selective activation of the SSE, and expression of the transgene thereby minimising off-target toxicity.
  • the transcription factor is differentially expressed in the target cell, i.e.
  • SSE also provides high expression of the transgene, preferably approaching or equivalent to the expression of the transgene when using a strong promoter, such as the full-length cytomegalovirus (CMV) promoter.
  • CMV cytomegalovirus
  • SSEs are highly selective, strong and may be small in size (preferably less than 500 base pairs). These provide a 'switch' in gene expression for associated open reading frames/transgenes from minimal expression to very strong expression depending on the cell type identity or state.
  • Enhancer and super-enhancer function may involve the presence of a promoter, such as a minimal promoter (e.g. minimal CMV), which contains key regions to facilitate recruitment of transcriptional machinery and typically contains a TSS.
  • a minimal promoter e.g. minimal CMV
  • transcription factor refers to a protein that binds to a regulatory element of a target gene to modulate, e.g. increase or decrease, expression of the target gene.
  • Transcription factors are often grouped based upon the type of DNA binding domain present in the TF. In eukaryotes, the most common DNA binding domains are zinc fingers, homeodomains, basic leucine zippers, and basic helix-loop-helix domains. TF paralogs with the same DNA binding domain often recognize similar DNA sequences.
  • the synthetic super-enhancers described herein may be bound by one or more transcription factors, i.e. one or more transcription factors bind to the SSE which results in activation.
  • Activation occurs via recruitment of RNA polymerase II, and thereby activates expression of an associated gene (i.e. the transgene), enhancing transcription above the level of expression by a promoter alone.
  • Binding of the transcription factor to the SSE may include the associated transcriptional and chromatin regulatory machinery.
  • the transcription factor is a developmental or stem-cell affiliated transcription factor. These types of transcription factors are associated with high levels of activation in stem cells or during the development of a cell.
  • the transcription factor is a transcription factor of the SOX family.
  • the SOX (SRY-related HMG box) gene family of transcription factors comprises 20 members in human and mouse genomes and all share a high-mobility-group (HMG) box domain.
  • the SOX family members with high homology are classified into groups: (SoxA, SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, SoxG and SoxH).
  • the transcription factor is a SoxB1 (i.e. SOX1, SOX2, SOX3) or SoxE (i.e. SOX8, SOX9, SOX10) transcription factor.
  • SOX2 has emerged as critical regulator of cancer stem cells (Bulstrode et al. 2017, Gangemi et al. 2009, Guerra-Rebollo et al. 2019, Lujan et al. 2012, D. K. Singh et al. 2017, S. K. Singh et al. 2004, and Boumahdi et al. 2014).
  • ChIP-seq datasets for glioblastoma stem cells (GSCs) and their differentiated progeny have been reported by Suva et al. 2014 who catalogued histone H3 enhancer marks (H3K27ac) marks and SOX2 binding unique to the GSCs.
  • H3K27ac histone H3 enhancer marks
  • the present inventors have identified a set of candidate SOX2-regulated enhancers operational in GSCs across diverse patient-derived lines. Therefore, in one embodiment, the transcription factor is SOX2.
  • Transcription factors bind by virtue of the DNA binding domain of the transcription factor binding to a specific motif (i.e. transcription factor binding site) in the target enhancer.
  • a transcription factor binding site sequence is 5-15 bp long.
  • the synthetic super-enhancer comprises at least one SOX dimer motif.
  • SOX dimer motif may be important for the function of an SSE in a target cell, for example many of the enhancer sequences described herein were shown to contain SOX dimer sites that were required to retain activity in glioblastoma stem cells.
  • Enhancer elements can contain SOX binding sites (sometimes palindromic sequences) where SOX transcription factors may homo- or heterodimerise. Typically, the spacing between each individual monomer binding motif would be around 8-12bp.
  • the SOX dimer motif comprises SEQ ID NO: 1: ACAAAGRGSVBYTKK where: R represents A or G; S represents C or G; V represents A, C or G; B represents C, G or T; Y represents C or T; and K represents G or T.
  • the SOX dimer motif comprises SEQ ID NO: 2: RRRRASARAGRRRBBHDDBWH where: R represents A or G; S represents C or G; B represents C, G or T; H represents A, C or T; D represents A, G or T; and W represents A or T.
  • the synthetic super-enhancer comprises at least one SOX motif.
  • the SOX motif is a SOX2 motif.
  • the SOX2 motif comprises SEQ ID NO: 3: WSARAGRSMYMHTBB where: W represents A or T; S represents C or G; R represents A or G; M represents A or C; Y represents C or T; H represents A, C or T; B represents C, G or T.
  • the synthetic super-enhancer comprises a sequence selected from: a SOX motif and/or a SOX dimer motif.
  • a super-enhancer refers to a cluster of enhancer sequences. Therefore, in one embodiment, the synthetic super-enhancer comprises two or more enhancer sequences. In a further embodiment, the synthetic super-enhancer comprises between two and eight enhancer sequences. In a yet further embodiment, the synthetic super-enhancer comprises four enhancer sequences.
  • Enhancer elements may be identified using techniques known in the art. For example, the methods described herein used ChIP-seq datasets for specific cell types to identify enhancers bound by transcription factors of interest or use of chromatin accessibility assays (e.g. ATAC-seq or MNase profiling). Publicly available resources are available to assist with genome-wide identification of active enhancers in various organisms and cell types, such as ENCODE or The Cancer Genome Atlas (TCGA) datasets.
  • TCGA Cancer Genome Atlas
  • the enhancer sequences present in the SSE do not all have the same sequence (i.e. the SSE is not a concatemer of the same enhancer element). Therefore, in one embodiment, the SSE comprises at least two different enhancer sequences. In one embodiment, each of the enhancer sequences has a different sequence. In one embodiment, each of the enhancer sequence is activated by the same transcription factor(s).
  • each of the enhancer sequences used in the SSE may be derived from different genes.
  • each of the enhancer sequences is derived from different genomic loci.
  • These enhancer sequences are all still preferably activated by a common transcription factor or set of cell type-affiliated transcription factor(s).
  • each of the enhancer sequences is activated by the transcription factor(s) and is derived from different genomic loci.
  • the synthetic super-enhancer comprises two or more, such as four enhancer sequences, derived from different genomic loci.
  • each of the enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus. This allows the context surrounding (i.e. directly upstream and/or downstream) the transcription factor binding site to be included in the enhancer sequence and therefore retain the enhancer function.
  • the enhancer sequence comprises between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 20 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 20 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor.
  • the enhancer sequence comprises between 50 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 50 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 50 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor. In a further embodiment, the enhancer sequence comprises between 80 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 80 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 80 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor.
  • each of the enhancer sequences within the synthetic super-enhancer are less than 500 nucleotides long, such as less than 450, 400, 350, 300, 250 or 200 nucleotides long. In a further embodiment, each of the enhancer sequences within the SSE are less than 300 nucleotides long. In one embodiment, each of the enhancer sequences within the synthetic super-enhancer are between 20 and 500 nucleotides long, such as between 50 and 250 nucleotides long or between 100 and 200 nucleotides long.
  • the enhancer sequence comprises between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, wherein the enhancer sequence is less than 500 nucleotides long. In a yet further embodiment, the enhancer sequence comprises between 20 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor, wherein the enhancer sequence is less than 300 nucleotides long.
  • each of the enhancer sequences within the SSE are about 160 nucleotides long.
  • 160 base pairs (bp) was chosen as this provides sufficient size for nucleosome binding and is considered to be an important attribute in the evolution of the grammar within functional enhancers.
  • 160 bp is a convenient size for synthesis of a pooled oligonucleotide library that incorporates 20 bp ends for subsequent construction of an arrayed plasmid library.
  • the synthetic super-enhancer is less than 2000 nucleotides long. In a further embodiment, the synthetic super-enhancer is less than 1500 nucleotides long, such as less than 1400, 1300, 1200, 1100, 1000, 950, 900, 850, 800, 750 or 700 nucleotides long. In one embodiment, the synthetic super-enhancer is less than 1200 nucleotides long. In a further embodiment, the synthetic super-enhancer is less than 700 nucleotides long. Preferably, the synthetic super-enhancer is less than 650 nucleotides long, such as 640 nucleotides long.
  • motifs described herein may be present in one or more of the enhancers of the SSE (for example, see Figure 8E ). Therefore, in one embodiment, one or more of the enhancers comprise a sequence selected from: a SOX motif and/or a SOX dimer motif.
  • each of the enhancer sequences within the synthetic super-enhancer comprises a SOX motif, such as a SOX2 motif. In one embodiment, each of the enhancer sequences within the synthetic super-enhancer comprises a SOX dimer motif.
  • the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif and/or at least one SOX dimer motif. In one embodiment, the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX2 motif. In one embodiment, the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif.
  • the one or more enhancer sequences comprise a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 4-63 (Table 1). In a further embodiment, the one or more enhancer sequences comprise a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 4-13 and 56-63. In a yet further embodiment, the one or more enhancer sequences have at least 85%, 90%, 95%, 97%, 99% sequence identity or are 100% identical to a sequence selected from the group consisting of SEQ ID NO: 4-63 (such as SEQ ID NO: 4-13 and 56-63).
  • the enhancer sequences described herein i.e.
  • Table 1 may be modified by at least one (such as less than 20, less than 10, less than 5) nucleotide substitution, deletion or addition, wherein the variant enhancer sequence substantially retains the functional characteristics of the sequence. It will be understood that variants of the enhancer sequences provided herein are still intended to retain the functional activity of the described enhancer sequences. For example, Example 4 shows that the described enhancer sequences had a more than 10-fold increase over mCMV when tested using the Nanoglo DLR assay. Therefore, the variant enhancer sequences included within this scope should not have an activity that is less than 75% of the activity of the starting sequence.
  • the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1. Therefore the SSE may comprise one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-63. Data is presented herein that shows arrangement of these enhancer sequences in multi-part arrays can increase transcriptional activity, without compromising cell specificity.
  • the synthetic super-enhancer comprises between one and eight, between two and six, or between three and five enhancer sequences selected from the sequences presented in Table 1.
  • the synthetic super-enhancer comprises four enhancer sequences selected from the sequences presented in Table 1.
  • the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-36. In an alternative embodiment, the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 37-63, more preferably SEQ ID NO: 54-63.
  • the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-13 and 54-63.
  • the SSE comprises four enhancer sequences selected from the group consisting of SEQ ID NO: 4-36, such as 4-13, in particular 4-8.
  • the SSE comprises four enhancer sequences selected from the group consisting of SEQ ID NO: 37-63, preferably four enhancer sequences selected from the group consisting of SEQ ID NO: 54-63, more preferably four enhancer sequences selected from the group consisting of SEQ ID NO: 56-63.
  • the SSE may comprise a sequence as described in Table 2.
  • the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80.
  • the sequence has at least 85%, 90%, 95%, 97%, 99% sequence identity or is 100% identical to a sequence selected from the group consisting of SEQ ID NO: 64-80.
  • the SSE comprises SEQ ID NO: 70. Variants of the sequences provided herein are still intended to retain the functional activity of the described SSE, i.e. transgene expression upon activation of the SSE by the transcription factor.
  • the "% sequence identity" between a first nucleotide sequence and a second nucleotide sequence may be calculated using NCBI BLAST v2.0, using standard settings for nucleotide sequences (BLASTN).
  • the "% sequence identity" between a first polypeptide sequence and a second polypeptide sequence may be calculated using NCBI BLAST v2.0, using standard settings for polypeptide sequences (BLASTP).
  • Polypeptide or polynucleotide sequences are said to be the same as or "identical” to other polypeptide or polynucleotide sequences, if they share 100% sequence identity over their entire length. Residues in sequences are numbered from left to right, i.e. from N- to C-terminus for polypeptides; from 5' to 3' terminus for polynucleotides.
  • a “difference" between sequences refers to an insertion, deletion or substitution of a single amino acid residue or nucleotide in a position of the second sequence, compared to the first sequence.
  • Two polynucleotide sequences can contain one, two or more such nucleotide differences.
  • Two polypeptide sequences can contain one, two or more such amino acid differences. Insertions, deletions or substitutions in a second sequence which is otherwise identical (100% sequence identity) to a first sequence result in reduced % sequence identity.
  • the number of additions, substitutions and/or deletions made to the first sequence to produce the second sequence may be ascertained.
  • An “addition” is the addition of one amino acid residue/nucleotide into the first sequence (including addition at either terminus of the first sequence).
  • a “substitution” is the substitution of one amino acid residue/nucleotide in the first sequence with one different amino acid residue/nucleotide.
  • a substitution may be conservative or non-conservative.
  • a substitution may be synonymous or nonsynonymous.
  • a “deletion” is the deletion of one amino acid residue/nucleotide from the first sequence (including deletion at either terminus of the first sequence).
  • the synthetic super-enhancer additionally comprises a transcriptional regulator, i.e. a sequence (or sequence encoding a protein) that controls gene expression.
  • a transcriptional regulator i.e. a sequence (or sequence encoding a protein) that controls gene expression.
  • a synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif.
  • a synthetic super-enhancer activated by SOX2 wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX motif and/or SOX dimer motif.
  • the SSE may be present in a construct comprising additional elements forming a functional nucleic acid molecule. Therefore, according to a further aspect of the invention, there is provided a functional nucleic acid molecule comprising the synthetic super-enhancer as described herein, operably linked to a transgene.
  • a functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
  • the functional nucleic acid molecule may comprise additional components to the SSE and transgene.
  • the synthetic super-enhancer may be operably linked to a promoter. Suitable promoters are known in the art. In one embodiment, the promoter is a minimal CMV promoter.
  • the SSEs may be used to enhance the expression of a transgene.
  • the transgene is a sequence encoding a product which is useful in biology and medicine, such as a prophylactic or a therapeutic transgene, e.g. protein or non-protein encoding oligonucleotide. Therefore, the transgene may encode a therapeutic payload.
  • the therapeutic payload may include: a therapeutic protein, such as an antigen, antibody, cytokine (e.g. to induce an immunogenic response), onco-suppressor protein (e.g. natural/unmutated p53), a differentiation factor (i.e.
  • the transgene encodes a non-protein encoding oligonucleotide, such as an RNA (other than mRNA), for example miRNA, siRNA, shRNA or IncRNA. It will be understood that transgenes encoding non-coding RNAs may be used in methods of gene silencing.
  • RNA other than mRNA
  • transgenes encoding non-coding RNAs may be used in methods of gene silencing.
  • the functional nucleic acid molecule comprises one or more transgenes. Therefore, it will be understood to a person skilled in the art that different combinations of transgenes may be included.
  • a method of expressing a transgene in a target cell which comprises expressing a transgene operatively linked to a synthetic super-enhancer as described herein wherein one or more of said transcription factors are expressed in the target cell.
  • the transgene operably linked to the SSE may encode an adverse payload.
  • the term "adverse payload” as used herein refers to a payload that has a negative impact upon the target cell.
  • the negative impact may be, for example, a negative effect on the health or viability of the cell and/or the ability of the cell to divide.
  • the adverse effect may be achieved directly (e.g. the transgene encodes a harmful substance to the cell, such as a proapoptotic gene or a suicide gene) or indirectly (e.g. the transgene encodes a substance that recruits an external factor that causes a harmful effect on the cell).
  • the adverse payload may be used to stimulate an immune response having a negative impact upon the target cell. Such a response may, for example, alter the local immune microenvironment.
  • the adverse payload encodes a protein that stimulates an immune response that leads to the activation of cytotoxic immune cells.
  • the adverse payload is selected from: a chemokine, cytokine, antibody or other immune modulatory protein.
  • the adverse payload is a pro-inflammatory cytokine, such as a cytokine selected from: IL-12, IL-10, IL-2, IFN- ⁇ and GM-CSF.
  • the adverse payload may be a cytokine such as IL-12 which has been shown to have anticancer activity.
  • IL-12 cause induction of IFN- ⁇ production by resting and activated CD4+ T cells, CD8+ T cells, and natural killer (NK) cells, as well as enhancing the proliferation of activated T and NK cells, increasing the lytic activity of NK/lymphokine-activated killer cells, and facilitating specific cytotoxic T lymphocyte (CTL) responses.
  • CTL cytotoxic T lymphocyte
  • IL-12 cannot be administered as a systemic treatment due to excessive toxicity, therefore a targeted therapy where expression only occurs within a target cell would enable the delivery of this payload.
  • an “immune response” is a measurable change in at least one cell, or one cell-type, or one endocrine pathway, or one exocrine pathway, of the immune system (including but not limited to a cell-mediated response, a humoral response, a cytokine response, a chemokine response).
  • an “immune cell” is defined as a cell of the immune system including, but not limited to, CD34+ cells, B-Cells, CD45+ (lymphocyte common antigen) cells, alpha-beta T-cells, cytotoxic T-cells, helper T-cells, plasma cells, neutrophils, monocytes, macrophages, dendritic cells, phagocytes, granulocytes, innate lymphoid cells, Natural Killer (NK) cells and gamma delta T-cells.
  • immune cells are classified with the aid of combinatorial cell surface molecule analysis (e.g., via flow cytometry) to identify or group or cluster to differentiate immune cells into sub-populations.
  • cytotoxic immune cell refers to immune cells that result in cell death, in particular cytotoxic T cells (also known as killer T cells).
  • the adverse payload encodes a cytotoxic substance (i.e. a cytotoxic payload).
  • the adverse payload is a suicide gene.
  • Suicide genes are genes that express a protein that causes cell death.
  • a suicide gene may require an externally supplied co-factor or co-drug (e.g. a prodrug) in order to work.
  • the co-factor or co-drug may then be converted by the product of the suicide gene into a cytotoxic entity.
  • the suicide gene encodes a protein capable of converting an inactive prodrug into a cytotoxic drug.
  • the inactive prodrug may be administered concomitantly or sequentially to the functional nucleic acid molecule.
  • the suicide gene is herpes simplex virus thymidine kinase (HSV-TK).
  • HSV-TK herpes simplex virus thymidine kinase
  • the HSV-TK gene is used in combination with the prodrug, ganciclovir (GCV) or an analogue thereof such as acyclovir and valacyclovir.
  • the suicide gene is cytosine deaminase (CD).
  • CD cytosine deaminase
  • the CD gene is used in combination with the prodrug 5-fluorocytosine (5FC).
  • the functional nucleic acid molecules described herein can be used to target a variety of cell types.
  • the cell is a mammalian cell, such as a human cell.
  • the invention may include the presence of an adverse payload, therefore is suited to target aberrant cells (i.e. an abnormal cell, such as a non-healthy cell).
  • the aberrant cell may be a hyperproliferative cell, i.e. a cell with excessive, abnormal proliferation.
  • the aberrant cell is a cancer cell or a neoplastic cell.
  • the adverse payload may be an anti-cancer payload.
  • SOX2 may also be amplified in other aberrant cells, particularly cancer cells, because it has been identified as an oncogene.
  • other aberrant cells that may be targeted using methods of the invention include squamous cell carcinomas of the lung and oesophagus, as well as many others.
  • the aberrant cell is a cancer cell selected from: a glioblastoma stem cell, a glioma cell, a lung cancer cell (in particular squamous lung cancer cell), an oesophageal cancer cell, an ovarian cancer cell, a breast cancer cell, an oral cancer cell (e.g. mouth, tongue, pharynx), a stomach cancer cell, a small intestine cancer cell, a colorectal cancer cell, a rectal cancer cell, a liver cancer cell, a bile duct cancer cell, a gall bladder cancer cell, a pancreatic cancer cell, a bone cancer cell (e.g.
  • osteosarcoma a skin cancer cell, a uterine cancer cell, a prostate cancer cell, a testicular cancer cell, a bladder cancer cell, a kidney cancer cell, a retinal cancer cell, a thyroid cancer cell, a lymphoma cell, a myeloma cell or a leukaemia cell.
  • the aberrant cell is a glioblastoma stem cell.
  • Glioblastomas are an aggressive form of glioma that is driven by elevated levels/activity of master regulatory neural stem cell-associated transcription factors.
  • Glioblastoma stem cells often have elevated expression or activity of key neurodevelopmental transcription factors, including SOX2, which is a key master regulator and reprogramming factor required for neural stem cell identity (Bulstrode et al. 2017, Gangemi et al. 2009, Guerra-Rebollo et al. 2019, Lopez-Bertoni et al. 2015, and MacLeod et al. 2019).
  • a vector comprising the synthetic super-enhancer or functional nucleic acid molecule as described herein.
  • vector is intended to refer to a molecule capable of transporting the functional nucleic acid molecule.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments may be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian and yeast vectors). Other vectors (e.g.
  • non-episomal mammalian vectors can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, “expression vectors”).
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.
  • Exemplary expression vectors are known in the art and may include, for example, plasmid vectors, viral vectors (for example adenovirus, adeno-associated virus, retrovirus or lentivirus vectors), phage vectors, cosmid vectors and the like.
  • viral vectors for example adenovirus, adeno-associated virus, retrovirus or lentivirus vectors
  • phage vectors for example adenovirus, adeno-associated virus, retrovirus or lentivirus vectors
  • cosmid vectors and the like.
  • the choice of expression vector may be dependent upon the type of host cell to be used and the purpose of use.
  • the vector is a viral vector.
  • Viral vectors particularly those used in gene therapy applications, are well known in the art. Such viruses may be RNA and DNA viruses with either single-stranded (ss) or double-stranded (ds) genomes.
  • viral vectors include, but are not limited to, adenoviruses, adeno-associated viruses (AAV), alphaviruses, flaviviruses, herpes simplex viruses (HSV), measles viruses, rhabdoviruses, retroviruses, lentiviruses, Newcastle disease virus (NDV), poxviruses and picornaviruses. Insert capacity and tropism can vary, therefore a viral vector may be chosen based upon the intended application.
  • AAV adeno-associated viruses
  • HSV herpes simplex viruses
  • NDV Newcastle disease virus
  • Insert capacity and tropism can vary, therefore a viral vector may be chosen based upon the intended application.
  • the vector is an AAV.
  • Different AAV serotypes differ in their tropism, therefore the type of AAV vector used can be chosen depending upon the type of tissue targeted.
  • the AAV vector may be selected from a number of serotypes known in the art, for example any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11, or may be a non-natural variant.
  • the AAV is selected from: AAV1, AAV2 or AAV5.
  • a vector comprising the synthetic super-enhancer as described herein and a transgene (i.e. a payload, such as a therapeutic payload).
  • a transgene i.e. a payload, such as a therapeutic payload.
  • the synthetic super-enhancer may be operably linked to other expression elements, such as a promoter.
  • the present invention also relates to compositions comprising the functional nucleic acid molecules or vectors described herein.
  • the composition may comprise components which enable delivery of said functional nucleic acid molecules by viral vectors (AAV, lentivirus and the like) and non-viral vectors (nanoparticles, lipid particles and the like).
  • viral vectors AAV, lentivirus and the like
  • non-viral vectors nanoparticles, lipid particles and the like
  • composition comprising the synthetic super-enhancer, functional nucleic acid molecule or the vector as described herein, and an acceptable carrier.
  • suitable carriers are known in the art, In certain embodiments, the carrier is selected based upon its ability to facilitate the transfection of a target cell with one or more functional nucleic acid molecules.
  • composition comprising the functional nucleic acid molecule or the vector as described herein, for use in therapy.
  • composition comprising the functional nucleic acid molecule or the vector as described herein, for use in the treatment of cancer.
  • nucleic acid molecule or vector or composition
  • the functional nucleic acid molecule as defined herein for the manufacture of a medicament, particularly for the treatment of cancer.
  • kits comprising the functional nucleic acid molecule as described herein, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug. Therefore, in this aspect, the kit additionally comprises the inactive prodrug (i.e. for administration with the functional nucleic acid molecule).
  • a method for treating a disease comprising administering the functional nucleic acid molecule, the vector or the composition according as described herein, to a patient.
  • references to "subject”, “patient” or “individual” refer to a subject, in particular a mammalian subject, to be treated.
  • Mammalian subjects include humans, non-human primates, farm animals (such as cows), sports animals, or pet animals, such as dogs, cats, guinea pigs, rabbits, rats or mice.
  • the subject is a human.
  • the subject is a non-human mammal, such as a mouse.
  • treating means reducing the frequency and/or severity of at least one sign or symptom of the disease or disorder experienced by a subject.
  • the disease is cancer.
  • Cancer refers to the abnormal growth or division of cells. Generally, the growth and/or life span of a cancer cell exceeds, and is not coordinated with, that of the normal cells and tissues around it. Cancers may be benign, pre-malignant or malignant. Cancers may also be primary cancers or secondary cancers. A primary cancer is the original organ or tissue where the cancer began, whereas a secondary cancer is the result of the primary cancer spreading (or metastasising) to another site in the body.
  • Cancer occurs in a variety of cells and tissues, including the oral cavity (e.g. mouth, tongue, pharynx), digestive system (e.g. oesophagus, stomach, small intestine, colon, rectum, liver, bile duct, gall bladder, pancreas), respiratory system (e.g. larynx, lung, bronchus), bones, joints, skin (e.g. basal cell, squamous cell, meningioma), breast, genital system (e.g. uterus, ovary, prostate, testis), urinary system (e.g. bladder, kidney, ureter), eye, nervous system (e.g. brain), endocrine system (e.g.
  • oral cavity e.g. mouth, tongue, pharynx
  • digestive system e.g. oesophagus, stomach, small intestine, colon, rectum, liver, bile duct, gall bladder, pancreas
  • respiratory system e.g.
  • hematopoietic system e.g. lymphoma, myeloma, leukaemia, acute lymphocytic leukaemia, chronic lymphocytic leukaemia, acute myeloid leukaemia, chronic myeloid leukaemia.
  • the cancer is a cancer located in the brain or spinal cord (i.e. the central nervous system), such as a primary or secondary cancer located in the central nervous system.
  • the invention finds particular use in the treatment of glioblastoma.
  • the functional nucleic acid molecule may be administered by any suitable mode of delivery for the intended treatment, such as intravenously, intraarterially, intracardially, intracutaneously, subcutaneously, interperitoneally, intramuscularly or orally.
  • the functional nucleic acid molecule, vector or composition is administered systemically. Administration may also be direct to the site of disease. Therefore, in one embodiment, the functional nucleic acid molecule, vector or composition is administered locally, e.g. directly into the organ or tissue, such as intratumorally.
  • a method for treating glioblastoma comprising administering a functional nucleic acid molecule and an inactive prodrug to a patient,
  • the inactive prodrug is administered concomitantly or sequentially to the functional nucleic acid molecule.
  • therapeutically effective amount is an amount that is effective to ameliorate or treat a symptom of a disease or disorder.
  • a therapeutically effective amount can be a "prophylactically effective amount” as prophylaxis can be considered therapy.
  • This destination vector design encompassed: the reporter gene cassette Nanoluc-Ires-mNGreen-pA and a minimal CMV promoter (mCMV).
  • mCMV minimal CMV promoter
  • the bacterial suicide ccdB cassette was used, for selection and efficient cloning.
  • CDV2 contained a ccdB cassette spanning the positions enabled assembly of up to four enhancers and spacers.
  • CDV2 also contains PiggyBactransposase recognition sites flanking the whole cassette.
  • GSC SOX2r1 and SOX2r2 were overlapped with DGC SOX2_H3K27ac (a H3K27ac Chip-Seq in an SOX2 overexpressing DGCs). Additionally, shared H3K27ac peaks were also identified between the GSC cell lines to define putative enhancer sequences. These shared peaks were individually overlapped with GSC specific SOX2r1 and GSC specific SOX2r2. This safeguarded against the loss of any potentially important regions. The resulting shared peaks were then combined into one file and peaks closer than 100 base pairs (bp) were merged which also removed duplicates.
  • the length of the peaks ranged from 15 - 5300 bp with an average length of 411 bp.
  • the pool was manually curated to remove repetitive sequences and non-enhancer sequences, such as centromeres. This resulted in a curated preliminary pool comprised of 1721 peaks ranging from 15 - 3366 bp and an average length of 402 bp.
  • GSCs were derived using NSC culture conditions previously reported by Pollard et al. Briefly, cells were expanded in serum and feeder free conditions in a neural basal media with N2 and B27 supplements. Cells were grown adherently by supplementing the culture media with Laminin-1. GSC7 has been characterised by Stricker et al. HEK293 cells were obtained from the ATCC cell bank. All other GSC lines and huFb170 were derived in the Pollard lab (unpublished) and are being characterised as part of the Glioma Cellular Genetics Resource (www.gcgr.org.uk).
  • This oligonucleotide pool was PCR-amplified (using limited cycles to reduce bias and 'jackpot' products meaning products which are easier to amplify will overtake the oligonucleotide pool) and cloned into the expression vector by an efficient Golden Gate reaction. 4579 individual plasmids were then randomly picked, isolated and plated as an arrayed plasmid DNA library on 96 well plates (x48). The bacterial colony picking and production of plasmid minipreps were supported by the Edinburgh Genome Foundry (S. Rosser). This library was then screened using the optimised Nanoglo DLR assay (Nano-Glo Dual-Luciferase Reporter Assay, Promega) in 384 well format. Each plate was transiently transfected together with PGK-FFLuc in a 1:10 ratio into GSC7 cells. 2 days later a Nanoglo DLR assay was performed and assayed on a plate reader.
  • oligonucleotide pool was first amplified for 10 cycles with 0.25 ⁇ l (2.5 ng input) and 0.5 ⁇ l of this reaction were used for the following 15 cycle amplification, in order to reduce PCR bias.
  • SPRI Solid Phase Reversible Immobilization
  • the oligo was PCR-amplified using biotinylated primers.
  • the PCR product was then SPRI purified to remove biotinylated primer dimers.
  • These dsDNA fragments were incubated with nuclear extract from GSC7 and GSC328. They were then bound to streptavidin magnetic beads, washed three times and the frozen beads were sent for mass spectrometry analysis.
  • Cell lines were cultured at 37°C in 5% CO 2 . Cells were grown on uncoated cell culture plastic dishes. Glioblastoma stem cell lines were grown under serum free condition using previously reported conditions (Pollard et al., 2009). For passaging cell lines were rinsed with PBS and detached using Accutase for GSC or 0.5% Trypsin/EDTA for huFb170 and HEK293, respectively. Cells were taken up in wash media and spun down at 300 xg for 3 min. They were resuspended in their respective growth media and replated. For cryo-preservation cells were resuspended in their growth media supplemented with 10% DMSO and stored at -80°C for short-term storage. For long-term preservation vials were transferred to liquid nitrogen containers.
  • HEK293 cells were seeded at the specified density in the respective plate format. The next day GMEM, DNA and PEI (homemade) are mixed and incubated for 15 min at room temperature to allow for complex formation. The transfection mix is subsequently dropped on the cells and analysis was carried out two days later.
  • This assay consists of two steps. The transfection was carried out using a normalisation plasmid PGK-Firefly-Luciferase (Promega, E5011) that was transfected in a 1/10 ratio with the plasmid of interest. First, the Firefly Luciferase activity is measured which allows to normalise to transfection efficiency. In a second step, the activity of Nanoluc is determined which is the readout of the plasmid of interest. Cells were washed 3x with PBS and 20 ⁇ l was left in the 96 well plate after the final wash (25 ⁇ l in 384 well). Oneglo buffer was added and the plate was shaken for 5 min at 480 rpm to allow cell lysis.
  • Nanoluc reaction was normalised to Firefly reaction to account for well-to-well variability of transfection efficiency. Normalised data were used to calculate the fold change to the empty vector control mCMV.
  • Cells were washed twice with PBS and fixed in 4% PFA for 10 min. Cells were permeabilised with 0.1% Triton-100 in PBS (further referred to as PBST). They were blocked with blocking solution (1% BSA in PBST with 3% goat serum) and incubated with the primary antibody at 4°C overnight (Table 3). The next day cells were washed 3x in PBST and the respective secondary antibody was applied in blocking solution and incubated for 45-60 min at room temperature. Cells were washed with PBS and incubated for 5 min with a DAPI nuclear counterstain at 1 ⁇ g/ml final concentration. Images were acquired using the Nikon TiE Microscope and NIS elements software (Nikon).
  • flow cytometry For flow cytometry, cells were detached, pelleted and resuspended in an appropriate volume of flow cytometry buffer (1% BSA in PBS, v/v). Cells were stained with Draq7 (Abcam, ab109202, f.c. 0.1 ⁇ M) as a live/dead stain and analysed using the BD LSRFortessa cell analyser (4 lasers, BD Bioscience). Analysis of flow cytometry data was carried out in the FlowJo Analysis software (FlowJo, version 10.6.2).
  • qRT-PCR For qRT-PCR the TaqMan Universal PCR Master Mix (Applied Biosystems) and the TaqMan gene expression assays (Life Technologies) were used on a Quant Studio7 Flex Real-Time qPCR machine. RNA samples which did not undergo reverse transcription to assess DNA contamination and water controls were employed on every plate. Additionally, qRT-PCR was carried out in technical duplicates. Data analysis was performed using the ddCt method which assumes 100% PCR efficiency and is guaranteed with TaqMan assays. Briefly, the mean was calculated for technical replicates and normalised to the housekeeping gene GAPDH which yields the ddCt value. These values were further normalised to a calibrator sample (GSC7) to give the ddCt.
  • GAC7 calibrator sample
  • Vectors were designed and produced according to Martella et al. 2017. Briefly, for the domestication of a new part, BsaI and BsmBI sites were removed. The new part was PCR amplified using primers generating an overhang for the fusion sites and BsaI site. This ensured simple and efficient cloning into the part entry vector. All part entry vectors contain a red fluorescent protein (RFP) which is recombined with the to be cloned part, thus, increasing the cloning efficiency as only white colonies can contain the part.
  • RFP red fluorescent protein
  • To assemble an expression vectors all parts are mixed with the acceptor vector in an equimolar ratio. To increase cloning efficiency the acceptor vector contains the bacterial suicide cassette ccdB which is recombined with the part of the expression vector. Therefore, bacteria which take up the unmodified acceptor will not be able to make colonies.
  • Cells were scraped in PBS and spun down at 0.3 g twice to remove all liquid. Cell pellets were resuspended in 70 ⁇ l of RIPA buffer (50 mM Tris-HCI pH 8.0 , 150 mM NaCl, 1% NP-40, 0.5% deoxycholate, 0.1% SDS and protease inhibitor (Complete, Roche, 11697498001) and incubated for 5 min on ice. Lysates were centrifuged at 13000 rpm for 10 min at 4°C (centrifuge 5415D, Eppendorf). And the supernatant was collected in a new tube. Protein extracts were quantified using the Pierce BCA Protein Assay Kit (Thermo Scientific, Cat: 23225) according to the manufacturer's instructions.
  • TBS-T 5% milk in TBS-T (TBS + 0.1% Tween-20) was used for membrane blocking for 1 hour at room temperature, followed by primary antibody incubation in 5% milk in TBS-T while rocking overnight (Table 4). The next morning, the membrane was washed three times with 5 min washed at room temperature in TBS-T and incubated with secondary antibody coupled to horseradish peroxidase in 5% milk in TBS-T at room temperature for 1 hour (Table 4).
  • the membrane was washed three times for 5 min in TBS-T and developed using homemade enhanced chemiluminescence (ECL) solution or Clarity ECL Western Blotting substrate (Bio-Rad, Cat:170-5061) and imaged using X ray films or a Bio-Rad ChemiDoc TM Imager.
  • ECL enhanced chemiluminescence
  • Clarity ECL Western Blotting substrate Bio-Rad, Cat:170-5061
  • Table 4 List of antibodies used in western blotting experiments Antibody Dilution Supplier/Catalogue number Primary antibodies Anti-SOX2 (rabbit) 1:1000 Abcam (ab92494) Anti-SOX9 (rabbit) 1:500 Millipore (ab5535) Anti-GAPDH (mouse) 1:10000 Ambion (AM4300) Secondary antibodies Anti-rabbit 1:5000 Novex (A16110) Anti- mouse 1:5000 Novex (A16027)
  • the pellet was then resuspended in 5 ml per 40 million cells of ice cold buffer A (10 mM HEPES pH 7.9, 1.5 mM MgCl 2 , 10 mM KCI, 0.5 mM DTT, protease inhibitors (Complete, Roche, 11697498001)) and incubated on ice for 10 min.
  • the cell suspension was transferred to a glass Dounce homogenizer and dounced 40 times on ice.
  • the cell suspension was transferred to a falcon and centrifuged at 1350 rcf for 10 min at 4°C.
  • the supernatant was discarded (cytosolic extract) and the pellet resuspended in 100 ⁇ l per 10 million cells in ice cold buffer B (20 mM HEPES pH 7.9, 5% glycerol, 1M NaCl, 1.5 mM MgCI2, 0.2 mM EDTA pH 8.0, 0.5 mM DTT, protease inhibitors (Complete, Roche, 11697498001)).
  • the suspension was rotated for 30 minutes at 4°C and transferred into a dialysis membrane (SnakeSkin, Thermo Scientific, Cat 68100).
  • Dialysis was carried out in 500 ml of dialysis buffer (20 mM HEPES pH 7.9, 5% glycerol, 100 mM KCI, 0.83 mM EDTA pH 8.0, 1.66 mM DTT, protease inhibitors (Complete, Roche, 11697498001)) for two hours at 4°C with rotation. Dialysis buffer was changed (500 ml) and the dialysis was continued overnight at 4°C. The extract was collected in an 1.5 ml tube and spun at maximum speed for 15 min at 4°C (centrifuge 5415D Eppendorf). The supernatant was collected into new 1.5 ml tubes and quantified (Pierce BCA Protein Assay Kit, Thermo Scientific, Cat 23225). 100 ⁇ g aliquots were flash frozen in liquid nitrogen and stored at -80°C.
  • dialysis buffer 20 mM HEPES pH 7.9, 5% glycerol, 100 mM KCI, 0.83 mM EDTA pH 8.0,
  • Enhancers were amplified with 5' biotinylated primers (Table 5) using PrimeStar Max (Takara) according to the manufacturer's instructions. Table 5: 5' Biotinylated primers for transcription factor pull down Primer number Sequence SEQ ID NO. Forward primer 595 TGATCCGTCTCgCCCTactaggttactggtgcatgc 81 Reverse primer 596 ACTAACGTCTCgGAGCacccaaactattggagcgag 82
  • PCR purification using Agencourt AMPure XP magnetic beads was carried out according to the manufacturer's instructions.
  • PCR product quantification using Tapestation and reagents was carried out according to manufacturer's instructions.
  • Streptavidin Magnetic Bead (NEB, S1420S) were used according to the manufacturer's instructions. Briefly, 10 ⁇ l beads were aliquoted into LoBind tubes and washed three times with binding buffer (20 mM Tris-HCI pH 7.5, 0.5 M NaCl, 1 mM EDTA) on the magnetic stand. 20 ⁇ l biotinylated DNA ( ⁇ 20 pmol) were mixed with 200 ⁇ l binding buffer and was added to the beads. The suspension was rotated at room temperature for 2 hours. The beads were washed again three times with binding buffer and 50 ⁇ g nuclear extract was added (total volume 50 ⁇ l).
  • binding buffer 20 mM Tris-HCI pH 7.5, 0.5 M NaCl, 1 mM EDTA
  • proteins were eluted in 20 ⁇ l loading buffer (lithium dodecyl sulfate (LDS) buffer containing 50 mM DTT) and boiled for 5 min to denature the proteins.
  • LDS lithium dodecyl sulfate
  • Zygotes were injected at the one-cell stage of development. Eggs were kept in 1.5% Agarose (Sigma) moulds as described by Nusslein-Volhard and Dahm 2002 for microinjection. Microinjection needles were pulled from glass capillaries (Harvard Apparatus, USA) using the P-97 Flaming/Brown Micropipette Puller (Sutter Instruments, USA). Needle pull parameters are as follows: Heat: 550; Pull: 200; Velocity: 55; Time: 150. Microinjection was performed on the PV820 Pneumatic PicoPump (World Precision Instruments [WPI], USA) system. DNA constructs were created using the Tol2Kit system (Kawakami 2007, Kwan et al. 2007).
  • plasmid DNA (30 ng/ ⁇ L) containing Tol2 capped mRNA (20 ng/ ⁇ L), supplemented with 0.2% w/v phenol red (Sigma) to facilitate visualization of injected volume, were injected.
  • Embryos were imaged at 24-48 hpf on a wide-field fluorescent microscope live following anaesthesia with Tricaine.
  • AAV Adeno-associated virus
  • HEK293 cells are seeded the day before the transfection into a 6 well plates so that on the day of transfection confluence would be at 60-70%.
  • a media change is carried out as this media will be conditioned with virus over the for two days.
  • the following days HEK293 or GSC7 cells are seeded at low density (10-20%) in the same or a smaller plate format (6 or 12 well plate).
  • AAV-conditioned media is spun down at 1300 rpm for 4 min to remove contaminating cells and the supernatant is transferred to the HEK293 cells seeded at low density. Cells are analysed on the microscope or flow cytometry.
  • Lyophilised GCV was diluted in DMSO to achieve 100mM stock concentration. GCV stocks were aliquoted and were stored at -20°C for no longer than 1 month. To make a working stock concentration, GCV was diluted 1:100 in appropriate culture media and then 20 ⁇ L of such working stock was added to wells already containing 80 ⁇ L of culture media (achieving another 1:5 dilution). Final concentration of GCV on cells was 200 ⁇ M).
  • DMSO was diluted 1:100 in appropriate culture media to achieve working stock. 20 ⁇ L of working stock was added to wells already containing 80 ⁇ L culture media. As positive control, 20 ⁇ L of DMSO was added to wells with 80 ⁇ L of culture media, achieving final concentration of 20% DMSO.
  • enhancers typically ⁇ 500-800bp
  • GSC glioblastoma stem cell
  • SSEs 'synthetic super-enhancers'
  • G7 cells can be efficiently differentiated into an astrocyte-like cells following exposure to foetal calf serum (FCS) over a 10-15 day period.
  • FCS foetal calf serum
  • GSCs G7 were therefore stably transfected with the SSE-T4 expression cassette (using the PiggyBac transposase system) and mNGreen+ cells sorted using fluorescence activated cell sorting (FACs). These were plated into 5% FCS the following day and mNGreen expression was measured every 5 days using flow cytometry over a 15 day time-course ( Figure 1H-J ).
  • 160 bp was chosen as this provides sufficient size for nucleosome binding and is likely to be an important attribute in the evolution of the grammar within functional enhancers (Soufi et al. 2015). Moreover, 160 bp is a convenient size for synthesis of a pooled oligonucleotide library that incorporates 20 bp ends for subsequent construction of an arrayed plasmid library. We favoured an arrayed plasmid library constructed from synthetic oligonucleotides, over other pooled library screening strategies, such as STARR-seq (Muerdter et al. 2018, Arnold et al. 2013), as this ensures improved signal to noise and straightforward validation of hits.
  • STARR-seq Muerdter et al. 2018, Arnold et al. 2013
  • the SOX2 enhancer library was screened in 384-well format using optimised luciferase assays. 135 plasmids were identified as functional with more than 10-fold increase over mCMV. 52 of these 135 initial hits were then validated using independent Nanoglo DLR assays in triplicate ( Figure 2 ). 16 of these 52 were found more than once. Hits were sanger-sequenced, confirmed to contain an enhancer and mapped back to the human genome with an expected fragment from the original designed set.
  • ID1101 is located in an intron of PRCP; ID2904 is located in the intronic region of the MYO18 gene and in proximity to SEZ6L; ID0109 is located in a gene-rich region between TPK1 and CNTNAP2; ID4328 is in the intronic region of the zinc finger transcription factor ZNF438. ID0876 is located in the intronic region of NWD2.
  • Table 7 Predicted target genes and distance from enhancer fragment to transcription start site (TSS) Fragment hg19 Gene 1 Distance to TSS1 for Gene 1 Gene 2 Distance to TSS2 for Gene 2 ID1101 chr11:82553160-82553319 PRCP 58265 ID2904 chr22:26319890-26320049 SEZ6L -245631 MYO18B 181790 ID0109 chr7:145217558-145217717 TPK1 -684464 CNTNAP2 -595843 ID4328 chr10:31308050-31308209 LYZL2 -389438 ZNF438 12737 ID0876 chr4:37394656-37394815 RELL1 293256 ID2339 chr8:1845248-1845407 MYOM2 -147864 ARHGEF10 73149 ID1737 chr15:38880930-38881 068 THBS1 -992325 RASGRP1 -239
  • GSC7 cells were stably transfected using the Piggybac transposase system and sorted for mNGreen+ cells. A similar number of live cells was sorted for the mCMV and untransfected controls. Cells were then placed into media containing no growth factors but 5% FCS to induce astrocytic differentiation.
  • Zebrafish are well-suited as an experimental model to explore the tissue specificity of enhancers.
  • We identified tissues which are shared between all constructs like ventral spinal cord expression, otic placode as well as midbrain/hindbrain and anterior forebrain. Some fragment had additional activity, such as the anterior/posterior intestine.
  • We observed broad, unspecific expression of EGFP in the CMV control and no expression in the mCMV using the same assay ( Figure 4 ).
  • the mCMV control exhibited green fluorescent eyes which is probably due to spurious transcription from the Crystal eye promoter ( Figure 4K ).
  • EXAMPLE 8 - SSEs can be used in adeno-associated viruses to induce selective killing of GSCs
  • GSC7 and huFB170 cell lines were transduced GSC7 and huFB170 cell lines with the adeno-associated virus 2 (AAV2) containing the suicide gene thymidine kinase (TK) derived from the Herpes simplex virus (HSV) in a polycistronic mRNA with the reporter gene mCherry joined by p2A.
  • AAV2 adeno-associated virus 2
  • TK thymidine kinase
  • HSV Herpes simplex virus
  • HSV-TK is a well-established prodrug which metabolises the non-cytotoxic prodrug ganciclovir (GCV) into a cytotoxic product by phosphorylation.
  • GCV non-cytotoxic prodrug ganciclovir
  • Phosphorylated GCV competes with dGTP as a substrate for polymerase thereby leading to interference of DNA synthesis causing premature termination and cytotoxicity.
  • MTT assay data demonstrates loss (or lack) of metabolic activity, which serves as an approximate readout for cell viability in GSC7 cells treated with CMV or SSE-7-driven TKv5-P2A-mCherry and GCV ( Figure 6B ).
  • ganciclovir alone on GSC7 cell viability (89% viability).
  • Live cell imaging confirmed these findings showing lower cell density and morphological changes linked to cellular stress, damage or death (rounded cells) after treatment ( Figure 6C ).
  • both CMV and SSE-7 can drive expression of HSV-TK-v5-P2A-mCherry construct to a sufficient level in GSC7 cells to induce cell death in the presence of ganciclovir.
  • EXAMPLE 9 - SSEs show activity in a range of GSCs
  • Example 8 It is desirable for an SSE in a proposed gene therapy to be expressed highly across diverse patient-derived glioblastoma cell lines, but inactive in other cell types.
  • the experiment described in Example 8 was repeated in five patient-derived glioblastoma cell lines (E17, E21, E28, E31, E34). These lines were selected for this experiment as they cover a spectrum of genetic and transcription GBM subtypes and have been shown to be tumour inducing in a mouse brain.
  • SSE7 is active in all cell lines, but to different degrees: it is highly expressed and comparable to full-length CMV in the positive control cell line GSC7 ( Figure 7C );and E17 and E28 ( Figure 7C ), which both belong to the classical subtype, but has a lower frequency of expression in E21, E31 and E34 ( Figure 7C ).
  • this dimer motif is a general feature of the oligonucleotide pool of sequences and mapped it to the Top 52 hits (all sequences with a 10x fold change over mCMV) compared to unconfirmed hits of the validation and in 10 random sequences of the initial oligonucleotide pool.
  • the motif is present at high frequency in the Top 32 hits and with lower frequency in the remaining Top 33-Top 52.
  • EXAMPLE 11 A SOX dimeric motif is essential for the activity of ID2904 in GSCs and suggests cooperation of SOX2 and SOX9 at key GSC functional enhancers
  • EXAMPLE 12 A SOX dimer motif helps to filter for active enhancers in silico
  • An additional screen with 209 enhancers was carried out to identify further active enhancers.
  • the enhancers were reduced to 160 bp based on their predicted motifs (termed minCSEs - see Table 1).
  • 160 bp enhancer fragments were mixed from different target genes to cover pathways like proliferation, stemness or brain-enriched/brain-specific or glioma-enriched/glioma-specific predicted target genes based on data from the human protein atlas (https://www.proteinatlas.org/), to generate further SSEs for screening.
  • TFs critical transcription factors
  • associated enhancers Mapping of transcription factor binding sites, chromatin accessibility or enhancer-associated histone marks are widely used to search for critical transcription factors (TFs) and associated enhancers.
  • TFs critical transcription factors
  • associated enhancers bind rather promiscuously, and the functional enhancers represent only a minor subset.
  • combining an array of functional enhancer sequences can lead to the formation of synthetic super-enhancers.
  • SSEs synergistic increases of transcriptional activation without sacrificing cell type selectivity.
  • Our data therefore support that individual enhancers can be combined to create synthetic super-enhancers that retain selectivity, yet are extremely strong at driving transcription.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • General Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Toxicology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Virology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Epidemiology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Medicinal Preparation (AREA)

Abstract

The invention relates to synthetic super-enhancers activated by one or more transcription factors. In particular, the present invention describes synthetic super-enhancers that are activated by one or more transcription factors expressed in a target cell and used to express transgenes, such as adverse payloads, upon activation of the synthetic super-enhancer by the transcription factor(s).

Description

    FIELD OF THE INVENTION
  • The invention relates to synthetic super-enhancers activated by one or more transcription factors. In particular, the present invention relates to synthetic super-enhancers that are activated by transcription factors expressed in target cells and are coupled to an adverse payload in order to kill target cells upon activation. The invention also relates to synthetic super-enhancers activated by one or more transcription factors of the SOX family.
    • BACKGROUND OF THE INVENTION
  • There is great interest in identification of cell type-specific enhancers and promoters that can be deployed in gene therapies, particularly where a therapeutic protein cargo needs to be expressed in highly cell selective manner to ensure maximum dosing and reduced off target effects. However, current strategies have limited success, and must often make compromises in size, selectivity or strength.
  • Two distinct, yet complementary, strategies can be used to identify cell type specific enhancers. First, strong and selective natural enhancers for a cell type of interest may emerge from systematic functional genetic dissection of regulatory networks for the cell type or lineage of interest. Second, fully synthetic enhancers can be constructed based on artificially synthesized DNA binding motifs of the known key transcription factors (TFs). Databases of such motifs - typically around 5-10 base pairs long - have been defined based on biochemical assays for strongest binding, such as JASPAR (Jolma et al. 2013). These transcription factor binding motifs can be synthesized and screened in high throughout using pooled libraries (Jolma et al. 2013). However, there are drawbacks to each approach. Individual natural enhancers are typically not strong enough to be useful in phenotypic assays or limited by size constraints or inappropriate selectivity. Artificial promoters built upon concatemers of the transcription factor binding motifs can induce expression, but do not have the appropriate 'grammar' - the spacing, order and appropriate affinity - that exists in natural enhancer sequences and is required for recruitment of cooperating TFs and co-factors (Farley et al. 2015). These will therefore lack selectivity and robustness.
  • Promoter sequences, enhancer sequences and methods of identifying such sequences are described in the art, but these suffer from the drawbacks discussed above. WO2014066848 and US2014/0296218 describe natural super-enhancers that are claimed to be useful for modulating expression of cell type-specific genes and methods for identifying said super-enhancers. WO2017155973 describes synthetic enhancers for use in recombinant parvoviruses, particularly enhancers with reduced size to enable delivery of large genetic payloads. WO2012101191 describes designing promoters for selective expression of genes by using transcription factor binding site motif prediction to create minimized promoters based on these motifs.
  • Therefore, there remains a need in the art to provide enhancers that have suitable selectivity and activity to be used in therapeutic methods, such as gene therapies.
    • SUMMARY OF THE INVENTION
  • According to a first aspect of the invention, there is provided a synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
  • According to a further aspect of the invention, there is provided a functional nucleic acid molecule comprising the synthetic super-enhancer described herein, operably linked to a transgene.
  • According to a further aspect of the invention, there is provided a functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
  • According to a further aspect of the invention, there is provided a synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif.
  • According to a further aspect of the invention, there is provided a synthetic super-enhancer activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif.
  • According to a further aspect of the invention, there is provided a vector comprising the synthetic super-enhancer or the functional nucleic acid molecule as described herein.
  • According to a further aspect of the invention, there is provided a composition comprising the synthetic super-enhancer, the functional nucleic acid molecule or the vector as described herein, and an acceptable carrier.
  • According to a further aspect of the invention, there is provided a composition comprising the functional nucleic acid molecule described herein, for use in therapy.
  • According to a further aspect of the invention, there is provided a composition comprising the functional nucleic acid molecule described herein, for use in the treatment of cancer.
  • According to a further aspect of the invention, there is provided a kit comprising the functional nucleic acid molecule comprising an adverse payload as described herein, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug, and wherein the kit additionally comprises said inactive prodrug for administration with the functional nucleic acid molecule, vector or composition.
  • According to a further aspect of the invention, there is provided a method for treating cancer comprising administering the functional nucleic acid molecule or the composition as described herein, to a patient.
  • According to a further aspect of the invention, there is provided a method for treating glioblastoma comprising administering a functional nucleic acid molecule and an inactive prodrug to a patient,
    • wherein the functional nucleic acid comprises a synthetic super-enhancer activated by a SOX transcription factor and a suicide gene which encodes a protein capable of converting the inactive prodrug into a cytotoxic drug, and
    • wherein the suicide gene is expressed upon activation of the synthetic super-enhancer by the SOX transcription factor in glioblastoma cells.
    BRIEF DESCRIPTION OF FIGURES
    • FIGURE 1 : Candidate full-length enhancers identified from SOX2 ChIP-Seq peaks can act synergistically and are selectively active. (A) Schematic of the constructs driven by a mCMV and a candidate enhancer, illustrated by candidate enhancer 270. Activity of 14 candidate enhancers in GSC7 (B), or G328 (C), when upstream of mCMV; a full-length CMV promoter is provided as positive reference control. (D) Activity of candidate enhancers in HEK293 cells. (E) Schematics of enhancer 270 clustering. (F) Enhancer activity is highest when clustering 4 x 270 enhancers together. (G) Activity of clustered enhancer constructs in HEK293 cells. (H) Outline of selectivity in differentiating GSC. (I) Flow cytometry of the activity of SSE-T4 (referred to as '4x Top4' in panel K). (J) Live cell images of the activity in SSE-T4 (also referred to herein as SSE-4) in cells scored in panel (I). (K) Schematic of construct designs for testing of multiple enhancers combined. (L) Relative activity of constructs from panel K in luciferase assays in GSC7 (not to scale). Paired Two-way Anova, * = p-Value ≤0.05, ** = p-Value ≤0.01. Every dot represents a biological replicate.
    • FIGURE 2 : Functional enhancer screening of an arrayed plasmid library (∼4000 plasmids) using plate-based luciferase reporter assays. (A) Experimental outline of the enhancer screen. (B) Results for the enhancer screen (C) Validation of the 135 hits of the initial screen in Nanoluc DLR assay (D) Most of the hits (>10 greater than mCMV) lie in intronic regions. % of mNGreen+ cells for the Top 17 hits in (E) GSC7, (F) GSC328, (G) HEK293, (H) huFb710. MFI of mNGreen+ cells in (I) GSC7, (J) GSC328, (K) HEK293 and (L) huFb170.
    • FIGURE 3 : Comparison of synthetic super-enhancers with restriction enzyme adaptor cloning sites removed. (A) Summary of design for second generation synthetic super-enhancers - C1 represents generation 2a (974 bp) and Gb1 represents generation 2b (640 bp); A = 20bp adapter, adjacent white box = 90bp spacer; n = 3 biological replicates. Note: The apparent discrepancy in size is due to 6 x 4 bp cloning sites which is not accounted for in the scheme for simplicity. (B) Nanoglo DLR assay to compare generation 2a and generation 2b synthetic super-enhancers (with and without cloning sites/adaptors removed, respectively). (C) Percentage of mNGreen+ cells of Generation 2a and Generation 2b synthetic super-enhancers. (D) MFI of mNGreen+ cells in Generation 2a and Generation 2b synthetic super-enhancers. (E) Representative live cells images for Generation 2a and Generation 2b synthetic super-enhancers; 20x magnification, scalebar = 50 µm.
    • FIGURE 4 : SSE-7 has selectivity for GSCs and forebrain neural stem cells (NSCs). (A) Schematic of designs for four-part combinations comprising SSEs (SSE-1 through SSE-7; left numbers). (B) Flow cytometry confirms these all have activity at similar levels to CMV. (C) In HEK293 cells all SSEs are inactive. (D) In human fibroblasts (huFb170) all SSEs are inactive. (E) Live cell images for SSE-7 and controls during astrocytic differentiation using 5% FCS. (F) % of mNGreen+ cells of SSE-7 and controls in 5% FCS. (G) MFI of mNGreen+ cells for SSE-7 normalised to CMV expression at day 0. (H) Experimental outline for the assessment of SSE-7 in zebrafish embryos and larvae. (J) Injection control (I) Schematics of the construct used for this experiment. (K) Activity of generation 2a plasmids C1, C3, C5 and C7, (note: these correspond to the latter derivatives: SSE-1, 3, 5 and 7, respectively, and contain adapter sequences) at 24 and 48 hours post fertilisation (hpf).
    • FIGURE 5 : Flow cytometry and Western immunoblot results for SSE-7 driving expression of multiple proteins (a) Schematic of the expression cassette, illustrating both mCherry and HSV-TKv5 expression from SSE-7 in a polycistronic transcript (including a P2A self-cleaving peptide sequence). (b) Flow cytometry data showing mCherry expression levels following delivery of this nucleic acid with a viral delivery (AAV). (c) Quantitation of flow cytometry results to score % of positive mCherry expressing cells and (d, e and f) shows the gating strategy. (g) Western blot confirming HSV-TK protein expression (using a fused v5 C-terminal epitope tag for detection). (h) Quantification of Western blot results in (g).
    • FIGURE 6 : Cytotoxicity results from MTT assay and live Incucyte imaging. (a) Confluence change over time of human GSC7 cells transduced or non-transduced with CMV or SSE-7-driven TKv5-P2A-mCherry in presence of 200µM GCV, 0.2% DMSO (vehicle control) or 20% DMSO (positive control). (b) Summary of MTT assay data in GSC7 cells in described conditions. Each dot represents biological replicate. MTT values were normalized to vehicle control. Error bars represent SD (N=3). (c) Live images of GSC7 cells at day 3 and day 8 demonstrating cell number and morphological changes in cells transduced with constructs in presence of 200µM GCV. (d) Live images of huFB170 cells at day 17 demonstrating cell number and morphological changes in cells transduced with constructs in presence of 200µM GCV. (e) Summary of MTT assay data in huFB170 cells in described conditions. Each dot represents biological replicate. MTT values were normalized to vehicle control (N=1).
    • FIGURE 7 : Activity of SSE-7 in a range of GSCs. (A) Schematic of the expression cassette. (B) Experimental outline, (C) Results of % mCherry expression for individual cells across the various cell lines tested. GSC7 was the positive control cell line tested (from which the fragments were initially screened). E17, E28 (previously termed G328), E21, E31, E34 refers to the five additional patient-derived glioblastoma cell lines.
    • FIGURE 8 : A SOX dimer motif is a major contributor to activity and is bound by both SOX2 and SOX9. (A) SOX dimer motif as identified by MEME in our data set being enriched in the top 32 active fragments. (B) Dimeric SOXE motif from the TRANSFAC database (Huang et al. 2015). (C) Strongest motif found in known motifs by HOMER. (D) Mapping of the SOX dimer motif found in our dataset in putative enhancers that lacked transcriptional activity. (E) Mapping of the SOX dimer motif from (A) to the Top51 positive hits of the 1st generation screen confirms this motif is found at higher frequency. The activity of the fragments is shown on the left side. (F) DNA was PCR-amplified with biotinylated primers and incubated with nuclear extract. The pulled down elution was analysed by mass spectrometry to identify bound proteins. (G) Summary of proteins pulled down by ID1101 (top circle representing all human transcription factors). SOX2 is a shared target between two cell lines to interact with ID1101. Within the 11 shared hits across GSC7 and GSC328 are three proteins of interest (NOC2L, and DMAP1, which are both components of histone acetyltransferase complexes; TFIID, a key component of the basal transcription machinery); several SOX family member proteins were also isolated. SOX2 interacts selectively with ID1101 in (H) GSC7 and (I) GSC328. (J) SOX dimer motif variants (S9D1-10) of the wild-type (WT) sequence used to investigate activity. WT sequence included as SEQ ID NO: 83, S9D1 - S9D2 are included as SEQ ID NOs: 84-85, and S9D6-S9D9 are included as SEQ ID NOs: 86-89. Activity of SOX dimer motif mutants in (K) GSC7 and (L) GSC328. (M) SOX9 selectively interacts with ID1101 and ID2904. Sequence 599 is a random DNA negative control.
    • FIGURE 9 : A second generation screen of enhancers enriched in the SOX dimer motif that have putative target genes with brain or glioma affiliated expression was performed. (A) Selection of candidate enhancer for the screening of the second generation. (B) SOX dimer motif. (C) First and (D) second screen to identify active enhancers based on SOX dimer motif and candidate target genes. (E) Schematics of assembly of 2nd generation SSE and subsequent measurement of using a reporter gene assay. (F) Screen across 209 second generation SSE in (F) GSC7 and (G) huFb170.
    DETAILED DESCRIPTION
  • The present invention relates to novel synthetic super-enhancers (SSEs) and provides an innovative way of delivering transgenes, such as therapeutic and adverse payloads. Building upon advances in knowledge of cell type-specific gene regulation, the inventors reasoned it might be possible to create SSEs by artificially assembling enhancers that retain the core functional elements and transcription factor motifs within full length enhancers. Importantly, this includes utilizing the natural and functional flanking sequence surrounding the direct transcription factor motifs in these enhancers. This strategy aims to enable retention of the natural local transcription factor (TF) binding context for the key cell type-specific TFs (low affinity with appropriate spacing), but facilitates high concentrations of TF binding to trigger strong transcription, i.e., capturing the appropriate grammar (spacing, affinity and orientation of co-binding proteins) of the TF motifs within cell type specific enhancers, but boosting transcriptional activity by combining in multi-part arrays. As described herein, it was found that construction of SSEs using combinatorial assembly of functionally annotated enhancers, results in strong, yet highly cell type selective regulatory elements that will have many applications, most notably in gene therapies.
    • Synthetic super-enhancers
  • According to a first aspect of the invention, there is provided a synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
  • As used herein, "enhancer" refers to a short region (usually 50-1500 bp) of DNA which is bound by proteins (for example, transcription factors) to enhance transcription of a gene. Enhancers typically act as cis-regulatory elements but may also act in trans, and may activate more than one target gene. Due to DNA folding and conformation or through promotion of multi-molecular compartments (referred to as transcriptional hubs or condensates, which may form by phase separation) they can be located distally from the transcription start site (TSS) of the gene being regulated. In contrast, promoters are upstream of the TSS on the same DNA sequence proximal to the site of transcriptional initiation. Promoters will be bound by RNA polymerase II in order to initiate transcription.
  • H3K27Ac is a histone modification commonly found at enhancers and can be used to predict regions of enhancer activity. Determination of whether a sequence enhances gene transcription (and therefore may be referred to as an "enhancer") can be determined using methods known in the art, most typically using a plasmid based reporter assay.
  • Super-enhancers are also involved in the activation or regulation of transcription. In nature, the term "super-enhancer" refers to a sequence that contains clusters of multiple enhancers, usually spanning a region of 5-15kb. These "super-enhancers" are highly occupied by transcriptional coactivators, such as the Mediator complex, compared to the average enhancers. They exhibit greater activity than average enhancers, and are frequently involved in driving expression of cell type-specific genes involved in maintaining cell identity or disease state (see, for example, US2014/0296218 and US2014/0287932 , which are herein incorporated by reference in their entirety). It will be understood that reference herein to a "synthetic super-enhancer" (or "SSE") refers to a super-enhancer not found in nature, i.e. is an artificially constructed super-enhancer designed for the purposes described herein, which may exhibit features associated with natural super-enhancers. In particular, an SSE is an artificial construct comprising two or more enhancer sequences. The SSE may be highly enriched for transcription factor motifs to stimulate transcriptional activation. This enables SSE sequences to be shorter than natural super-enhancers because the high concentration of transcription factor binding to the SSE promotes transcriptional activity.
  • In one embodiment, the present invention provides an innovative way of delivering a transgene by coupling it to an SSE that is activated by a transcription factor - or unique combination of transcription factors - expressed in a target cell. Therefore, endogenous expression of the transcription factor(s) in the target cell is used to initiate expression of the exogenous transgene in a highly selective manner. Preferably, the transcription factor has cell type or lineage-specific expression patterns and is therefore minimally expressed in cells other than the target cell, i.e., it is not ubiquitously expressed. This enables cell-type or cell state selective activation of the SSE, and expression of the transgene thereby minimising off-target toxicity. In one embodiment, the transcription factor is differentially expressed in the target cell, i.e. compared to other cell types. The use of an SSE also provides high expression of the transgene, preferably approaching or equivalent to the expression of the transgene when using a strong promoter, such as the full-length cytomegalovirus (CMV) promoter. SSEs are highly selective, strong and may be small in size (preferably less than 500 base pairs). These provide a 'switch' in gene expression for associated open reading frames/transgenes from minimal expression to very strong expression depending on the cell type identity or state.
  • Enhancer and super-enhancer function may involve the presence of a promoter, such as a minimal promoter (e.g. minimal CMV), which contains key regions to facilitate recruitment of transcriptional machinery and typically contains a TSS.
  • As used herein, the term "transcription factor" refers to a protein that binds to a regulatory element of a target gene to modulate, e.g. increase or decrease, expression of the target gene. Transcription factors (TFs) are often grouped based upon the type of DNA binding domain present in the TF. In eukaryotes, the most common DNA binding domains are zinc fingers, homeodomains, basic leucine zippers, and basic helix-loop-helix domains. TF paralogs with the same DNA binding domain often recognize similar DNA sequences. The synthetic super-enhancers described herein may be bound by one or more transcription factors, i.e. one or more transcription factors bind to the SSE which results in activation. Activation occurs via recruitment of RNA polymerase II, and thereby activates expression of an associated gene (i.e. the transgene), enhancing transcription above the level of expression by a promoter alone. Binding of the transcription factor to the SSE may include the associated transcriptional and chromatin regulatory machinery.
  • In one embodiment, the transcription factor is a developmental or stem-cell affiliated transcription factor. These types of transcription factors are associated with high levels of activation in stem cells or during the development of a cell.
  • In one embodiment, the transcription factor is a transcription factor of the SOX family. The SOX (SRY-related HMG box) gene family of transcription factors comprises 20 members in human and mouse genomes and all share a high-mobility-group (HMG) box domain. The SOX family members with high homology are classified into groups: (SoxA, SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, SoxG and SoxH). In one embodiment, the transcription factor is a SoxB1 (i.e. SOX1, SOX2, SOX3) or SoxE (i.e. SOX8, SOX9, SOX10) transcription factor.
  • SOX2 has emerged as critical regulator of cancer stem cells (Bulstrode et al. 2017, Gangemi et al. 2009, Guerra-Rebollo et al. 2019, Lujan et al. 2012, D. K. Singh et al. 2017, S. K. Singh et al. 2004, and Boumahdi et al. 2014). ChIP-seq datasets for glioblastoma stem cells (GSCs) and their differentiated progeny have been reported by Suva et al. 2014 who catalogued histone H3 enhancer marks (H3K27ac) marks and SOX2 binding unique to the GSCs. In particular, the present inventors have identified a set of candidate SOX2-regulated enhancers operational in GSCs across diverse patient-derived lines. Therefore, in one embodiment, the transcription factor is SOX2.
  • Transcription factors bind by virtue of the DNA binding domain of the transcription factor binding to a specific motif (i.e. transcription factor binding site) in the target enhancer. Typically, a transcription factor binding site sequence is 5-15 bp long.
  • In one embodiment, the synthetic super-enhancer comprises at least one SOX dimer motif. Such motifs may be important for the function of an SSE in a target cell, for example many of the enhancer sequences described herein were shown to contain SOX dimer sites that were required to retain activity in glioblastoma stem cells. Enhancer elements can contain SOX binding sites (sometimes palindromic sequences) where SOX transcription factors may homo- or heterodimerise. Typically, the spacing between each individual monomer binding motif would be around 8-12bp.
  • In one embodiment, the SOX dimer motif comprises SEQ ID NO: 1:
    ACAAAGRGSVBYTKK
    where:
    R represents A or G; S represents C or G; V represents A, C or G; B represents C, G or T; Y represents C or T; and K represents G or T.
  • In a further embodiment, the SOX dimer motif comprises SEQ ID NO: 2:
    RRRRASARAGRRRBBHDDBWH
    where:
    R represents A or G; S represents C or G; B represents C, G or T; H represents A, C or T; D represents A, G or T; and W represents A or T.
  • In one embodiment, the synthetic super-enhancer comprises at least one SOX motif. In a further embodiment, the SOX motif is a SOX2 motif.
  • In one embodiment, the SOX2 motif comprises SEQ ID NO: 3:
    WSARAGRSMYMHTBB
    where:
    W represents A or T; S represents C or G; R represents A or G; M represents A or C; Y represents C or T; H represents A, C or T; B represents C, G or T.
  • In one embodiment, wherein the synthetic super-enhancer comprises a sequence selected from: a SOX motif and/or a SOX dimer motif.
  • As explained herein, a super-enhancer refers to a cluster of enhancer sequences. Therefore, in one embodiment, the synthetic super-enhancer comprises two or more enhancer sequences. In a further embodiment, the synthetic super-enhancer comprises between two and eight enhancer sequences. In a yet further embodiment, the synthetic super-enhancer comprises four enhancer sequences.
  • Enhancer elements may be identified using techniques known in the art. For example, the methods described herein used ChIP-seq datasets for specific cell types to identify enhancers bound by transcription factors of interest or use of chromatin accessibility assays (e.g. ATAC-seq or MNase profiling). Publicly available resources are available to assist with genome-wide identification of active enhancers in various organisms and cell types, such as ENCODE or The Cancer Genome Atlas (TCGA) datasets.
  • Preferably, the enhancer sequences present in the SSE do not all have the same sequence (i.e. the SSE is not a concatemer of the same enhancer element). Therefore, in one embodiment, the SSE comprises at least two different enhancer sequences. In one embodiment, each of the enhancer sequences has a different sequence. In one embodiment, each of the enhancer sequence is activated by the same transcription factor(s).
  • The data presented herein shows that assembly of enhancers derived from different genomic loci into 4-part arrays (-640 bp) surprisingly led to orders of magnitude increases in their activity without compromising selectivity. Therefore, each of the enhancer sequences used in the SSE may be derived from different genes. In a further embodiment, each of the enhancer sequences is derived from different genomic loci. These enhancer sequences are all still preferably activated by a common transcription factor or set of cell type-affiliated transcription factor(s). In one embodiment, each of the enhancer sequences is activated by the transcription factor(s) and is derived from different genomic loci. In one embodiment, the synthetic super-enhancer comprises two or more, such as four enhancer sequences, derived from different genomic loci.
  • In one embodiment, each of the enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus. This allows the context surrounding (i.e. directly upstream and/or downstream) the transcription factor binding site to be included in the enhancer sequence and therefore retain the enhancer function. In a further embodiment, the enhancer sequence comprises between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 20 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 20 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor. In a further embodiment, the enhancer sequence comprises between 50 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 50 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 50 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor. In a further embodiment, the enhancer sequence comprises between 80 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, such as between 80 and 300 nucleotides upstream and/or downstream of the binding site for the transcription factor or preferably between 80 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor.
  • In one embodiment, each of the enhancer sequences within the synthetic super-enhancer are less than 500 nucleotides long, such as less than 450, 400, 350, 300, 250 or 200 nucleotides long. In a further embodiment, each of the enhancer sequences within the SSE are less than 300 nucleotides long. In one embodiment, each of the enhancer sequences within the synthetic super-enhancer are between 20 and 500 nucleotides long, such as between 50 and 250 nucleotides long or between 100 and 200 nucleotides long.
  • It will be understood that this embodiments may be combined. Therefore, in a further embodiment, the enhancer sequence comprises between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor, wherein the enhancer sequence is less than 500 nucleotides long. In a yet further embodiment, the enhancer sequence comprises between 20 and 200 nucleotides upstream and/or downstream of the binding site for the transcription factor, wherein the enhancer sequence is less than 300 nucleotides long.
  • In a further embodiment, each of the enhancer sequences within the SSE are about 160 nucleotides long. In particular, 160 base pairs (bp) was chosen as this provides sufficient size for nucleosome binding and is considered to be an important attribute in the evolution of the grammar within functional enhancers. Moreover, 160 bp is a convenient size for synthesis of a pooled oligonucleotide library that incorporates 20 bp ends for subsequent construction of an arrayed plasmid library.
  • In one embodiment, the synthetic super-enhancer is less than 2000 nucleotides long. In a further embodiment, the synthetic super-enhancer is less than 1500 nucleotides long, such as less than 1400, 1300, 1200, 1100, 1000, 950, 900, 850, 800, 750 or 700 nucleotides long. In one embodiment, the synthetic super-enhancer is less than 1200 nucleotides long. In a further embodiment, the synthetic super-enhancer is less than 700 nucleotides long. Preferably, the synthetic super-enhancer is less than 650 nucleotides long, such as 640 nucleotides long.
  • The motifs described herein may be present in one or more of the enhancers of the SSE (for example, see Figure 8E). Therefore, in one embodiment, one or more of the enhancers comprise a sequence selected from: a SOX motif and/or a SOX dimer motif.
  • In one embodiment, each of the enhancer sequences within the synthetic super-enhancer comprises a SOX motif, such as a SOX2 motif. In one embodiment, each of the enhancer sequences within the synthetic super-enhancer comprises a SOX dimer motif.
  • In one embodiment, the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif and/or at least one SOX dimer motif. In one embodiment, the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX2 motif. In one embodiment, the synthetic super-enhancer is activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif.
  • In one embodiment, the one or more enhancer sequences comprise a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 4-63 (Table 1). In a further embodiment, the one or more enhancer sequences comprise a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 4-13 and 56-63. In a yet further embodiment, the one or more enhancer sequences have at least 85%, 90%, 95%, 97%, 99% sequence identity or are 100% identical to a sequence selected from the group consisting of SEQ ID NO: 4-63 (such as SEQ ID NO: 4-13 and 56-63). The enhancer sequences described herein (i.e. Table 1) may be modified by at least one (such as less than 20, less than 10, less than 5) nucleotide substitution, deletion or addition, wherein the variant enhancer sequence substantially retains the functional characteristics of the sequence. It will be understood that variants of the enhancer sequences provided herein are still intended to retain the functional activity of the described enhancer sequences. For example, Example 4 shows that the described enhancer sequences had a more than 10-fold increase over mCMV when tested using the Nanoglo DLR assay. Therefore, the variant enhancer sequences included within this scope should not have an activity that is less than 75% of the activity of the starting sequence.
  • In one embodiment, the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1. Therefore the SSE may comprise one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-63. Data is presented herein that shows arrangement of these enhancer sequences in multi-part arrays can increase transcriptional activity, without compromising cell specificity. In a further embodiment, the synthetic super-enhancer comprises between one and eight, between two and six, or between three and five enhancer sequences selected from the sequences presented in Table 1. In a yet further embodiment, the synthetic super-enhancer comprises four enhancer sequences selected from the sequences presented in Table 1.
  • In one embodiment, the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-36. In an alternative embodiment, the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 37-63, more preferably SEQ ID NO: 54-63.
  • In one embodiment, the SSE comprises one or more enhancer sequences selected from the group consisting of SEQ ID NO: 4-13 and 54-63.
  • In a further embodiment, the SSE comprises four enhancer sequences selected from the group consisting of SEQ ID NO: 4-36, such as 4-13, in particular 4-8. In an alternative embodiment, the SSE comprises four enhancer sequences selected from the group consisting of SEQ ID NO: 37-63, preferably four enhancer sequences selected from the group consisting of SEQ ID NO: 54-63, more preferably four enhancer sequences selected from the group consisting of SEQ ID NO: 56-63.
  • The SSE may comprise a sequence as described in Table 2. In one embodiment, the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80. In a further embodiment, the sequence has at least 85%, 90%, 95%, 97%, 99% sequence identity or is 100% identical to a sequence selected from the group consisting of SEQ ID NO: 64-80. In a yet further embodiment, the SSE comprises SEQ ID NO: 70. Variants of the sequences provided herein are still intended to retain the functional activity of the described SSE, i.e. transgene expression upon activation of the SSE by the transcription factor.
  • For the purposes of comparing two closely-related polynucleotide sequences, the "% sequence identity" between a first nucleotide sequence and a second nucleotide sequence may be calculated using NCBI BLAST v2.0, using standard settings for nucleotide sequences (BLASTN). For the purposes of comparing two closely-related polypeptide sequences, the "% sequence identity" between a first polypeptide sequence and a second polypeptide sequence may be calculated using NCBI BLAST v2.0, using standard settings for polypeptide sequences (BLASTP).
  • Polypeptide or polynucleotide sequences are said to be the same as or "identical" to other polypeptide or polynucleotide sequences, if they share 100% sequence identity over their entire length. Residues in sequences are numbered from left to right, i.e. from N- to C-terminus for polypeptides; from 5' to 3' terminus for polynucleotides.
  • A "difference" between sequences refers to an insertion, deletion or substitution of a single amino acid residue or nucleotide in a position of the second sequence, compared to the first sequence. Two polynucleotide sequences can contain one, two or more such nucleotide differences. Two polypeptide sequences can contain one, two or more such amino acid differences. Insertions, deletions or substitutions in a second sequence which is otherwise identical (100% sequence identity) to a first sequence result in reduced % sequence identity.
  • Alternatively, for the purposes of comparing a first, reference sequence to a second, comparison sequence, the number of additions, substitutions and/or deletions made to the first sequence to produce the second sequence may be ascertained. An "addition" is the addition of one amino acid residue/nucleotide into the first sequence (including addition at either terminus of the first sequence). A "substitution" is the substitution of one amino acid residue/nucleotide in the first sequence with one different amino acid residue/nucleotide. With respect to polypeptide sequences, a substitution may be conservative or non-conservative. In the context of polynucleotide sequences, a substitution may be synonymous or nonsynonymous. A "deletion" is the deletion of one amino acid residue/nucleotide from the first sequence (including deletion at either terminus of the first sequence).
  • In one embodiment, the synthetic super-enhancer additionally comprises a transcriptional regulator, i.e. a sequence (or sequence encoding a protein) that controls gene expression.
  • According to another aspect of the invention, there is provided a synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif. It will be understood that the embodiments described herein that apply to the synthetic super-enhancer of the functional nucleic acid molecule, also apply to this aspect of the invention.
  • According to a further aspect of the invention, there is provided a synthetic super-enhancer activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX motif and/or SOX dimer motif.
    • Functional nucleic acid molecules
  • The SSE may be present in a construct comprising additional elements forming a functional nucleic acid molecule. Therefore, according to a further aspect of the invention, there is provided a functional nucleic acid molecule comprising the synthetic super-enhancer as described herein, operably linked to a transgene.
  • According to a further aspect of the invention, there is provided a functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
  • The functional nucleic acid molecule may comprise additional components to the SSE and transgene. For example, the synthetic super-enhancer may be operably linked to a promoter. Suitable promoters are known in the art. In one embodiment, the promoter is a minimal CMV promoter.
    • Transgenes
  • As described herein, the SSEs may be used to enhance the expression of a transgene. In one embodiment, the transgene is a sequence encoding a product which is useful in biology and medicine, such as a prophylactic or a therapeutic transgene, e.g. protein or non-protein encoding oligonucleotide. Therefore, the transgene may encode a therapeutic payload. For example, the therapeutic payload may include: a therapeutic protein, such as an antigen, antibody, cytokine (e.g. to induce an immunogenic response), onco-suppressor protein (e.g. natural/unmutated p53), a differentiation factor (i.e. to modulate cell fate), or a protein with nucleic acid editing or gene activity modulation function (e.g. DNA or RNA editing, or transcriptional regulation). In an alternative embodiment, the transgene encodes a non-protein encoding oligonucleotide, such as an RNA (other than mRNA), for example miRNA, siRNA, shRNA or IncRNA. It will be understood that transgenes encoding non-coding RNAs may be used in methods of gene silencing.
  • In one embodiment, the functional nucleic acid molecule comprises one or more transgenes. Therefore, it will be understood to a person skilled in the art that different combinations of transgenes may be included.
  • According to a further aspect of the invention, there is provided a method of expressing a transgene in a target cell, which comprises expressing a transgene operatively linked to a synthetic super-enhancer as described herein wherein one or more of said transcription factors are expressed in the target cell.
    • Adverse payloads
  • As described herein, the transgene operably linked to the SSE may encode an adverse payload. The term "adverse payload" as used herein refers to a payload that has a negative impact upon the target cell. The negative impact may be, for example, a negative effect on the health or viability of the cell and/or the ability of the cell to divide. The adverse effect may be achieved directly (e.g. the transgene encodes a harmful substance to the cell, such as a proapoptotic gene or a suicide gene) or indirectly (e.g. the transgene encodes a substance that recruits an external factor that causes a harmful effect on the cell).
  • The adverse payload may be used to stimulate an immune response having a negative impact upon the target cell. Such a response may, for example, alter the local immune microenvironment. In one embodiment, the adverse payload encodes a protein that stimulates an immune response that leads to the activation of cytotoxic immune cells. In one embodiment, the adverse payload is selected from: a chemokine, cytokine, antibody or other immune modulatory protein. In a further embodiment, the adverse payload is a pro-inflammatory cytokine, such as a cytokine selected from: IL-12, IL-10, IL-2, IFN-α and GM-CSF. For example, the adverse payload may be a cytokine such as IL-12 which has been shown to have anticancer activity. IL-12 cause induction of IFN-γ production by resting and activated CD4+ T cells, CD8+ T cells, and natural killer (NK) cells, as well as enhancing the proliferation of activated T and NK cells, increasing the lytic activity of NK/lymphokine-activated killer cells, and facilitating specific cytotoxic T lymphocyte (CTL) responses. However, IL-12 cannot be administered as a systemic treatment due to excessive toxicity, therefore a targeted therapy where expression only occurs within a target cell would enable the delivery of this payload.
  • An "immune response" is a measurable change in at least one cell, or one cell-type, or one endocrine pathway, or one exocrine pathway, of the immune system (including but not limited to a cell-mediated response, a humoral response, a cytokine response, a chemokine response).
  • An "immune cell" is defined as a cell of the immune system including, but not limited to, CD34+ cells, B-Cells, CD45+ (lymphocyte common antigen) cells, alpha-beta T-cells, cytotoxic T-cells, helper T-cells, plasma cells, neutrophils, monocytes, macrophages, dendritic cells, phagocytes, granulocytes, innate lymphoid cells, Natural Killer (NK) cells and gamma delta T-cells. Typically, immune cells are classified with the aid of combinatorial cell surface molecule analysis (e.g., via flow cytometry) to identify or group or cluster to differentiate immune cells into sub-populations. In molecules and methods of the invention where the payload is an adverse payload, the stimulated immune response is intended to adversely affect the target cell. Reference to "cytotoxic immune cell" refers to immune cells that result in cell death, in particular cytotoxic T cells (also known as killer T cells).
  • In one embodiment, the adverse payload encodes a cytotoxic substance (i.e. a cytotoxic payload).
  • In one embodiment, the adverse payload is a suicide gene. Suicide genes are genes that express a protein that causes cell death. Alternatively, a suicide gene may require an externally supplied co-factor or co-drug (e.g. a prodrug) in order to work. The co-factor or co-drug may then be converted by the product of the suicide gene into a cytotoxic entity. In one embodiment, the suicide gene encodes a protein capable of converting an inactive prodrug into a cytotoxic drug. The inactive prodrug may be administered concomitantly or sequentially to the functional nucleic acid molecule.
  • In one embodiment, the suicide gene is herpes simplex virus thymidine kinase (HSV-TK). In particular, the HSV-TK gene is used in combination with the prodrug, ganciclovir (GCV) or an analogue thereof such as acyclovir and valacyclovir. In an alternative embodiment, the suicide gene is cytosine deaminase (CD). In particular, the CD gene is used in combination with the prodrug 5-fluorocytosine (5FC).
    • Target cells
  • The functional nucleic acid molecules described herein can be used to target a variety of cell types. In particular, the cell is a mammalian cell, such as a human cell. The invention may include the presence of an adverse payload, therefore is suited to target aberrant cells (i.e. an abnormal cell, such as a non-healthy cell).
  • The aberrant cell may be a hyperproliferative cell, i.e. a cell with excessive, abnormal proliferation. In one embodiment, the aberrant cell is a cancer cell or a neoplastic cell. In this embodiment, the adverse payload may be an anti-cancer payload.
  • SOX2 may also be amplified in other aberrant cells, particularly cancer cells, because it has been identified as an oncogene. Examples of other aberrant cells that may be targeted using methods of the invention include squamous cell carcinomas of the lung and oesophagus, as well as many others.
  • In one embodiment, the aberrant cell is a cancer cell selected from: a glioblastoma stem cell, a glioma cell, a lung cancer cell (in particular squamous lung cancer cell), an oesophageal cancer cell, an ovarian cancer cell, a breast cancer cell, an oral cancer cell (e.g. mouth, tongue, pharynx), a stomach cancer cell, a small intestine cancer cell, a colorectal cancer cell, a rectal cancer cell, a liver cancer cell, a bile duct cancer cell, a gall bladder cancer cell, a pancreatic cancer cell, a bone cancer cell (e.g. osteosarcoma), a skin cancer cell, a uterine cancer cell, a prostate cancer cell, a testicular cancer cell, a bladder cancer cell, a kidney cancer cell, a retinal cancer cell, a thyroid cancer cell, a lymphoma cell, a myeloma cell or a leukaemia cell.
  • In a particular embodiment, the aberrant cell is a glioblastoma stem cell. Glioblastomas are an aggressive form of glioma that is driven by elevated levels/activity of master regulatory neural stem cell-associated transcription factors. Glioblastoma stem cells (GSCs) often have elevated expression or activity of key neurodevelopmental transcription factors, including SOX2, which is a key master regulator and reprogramming factor required for neural stem cell identity (Bulstrode et al. 2017, Gangemi et al. 2009, Guerra-Rebollo et al. 2019, Lopez-Bertoni et al. 2015, and MacLeod et al. 2019). Knockdown of SOX2 in GSCs reduces their tumorigenicity (Gangemi et al. 2009), whereas its ectopic expression together with POU3F2, OLIG2 and SALL2 enforces the GSC state (Suva et al. 2014). The Examples presented herein show that GSC-selective SSEs retained activity in adeno-associated viruses (AAVs) and were used to drive expression of cytotoxic payloads for targeted killing of GSCs. Furthermore, the activity of SSEs was extinguished during differentiation of GSCs and absent in HEK or fibroblast cells. Therefore, GSC selective expression was retained even though the strength of the promoter has been massively increased.
    • Vectors
  • According to a further aspect of the invention, there is provided a vector comprising the synthetic super-enhancer or functional nucleic acid molecule as described herein.
  • The term "vector", as used herein, is intended to refer to a molecule capable of transporting the functional nucleic acid molecule. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian and yeast vectors). Other vectors (e.g. non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, "expression vectors"). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.
  • Exemplary expression vectors are known in the art and may include, for example, plasmid vectors, viral vectors (for example adenovirus, adeno-associated virus, retrovirus or lentivirus vectors), phage vectors, cosmid vectors and the like. The choice of expression vector may be dependent upon the type of host cell to be used and the purpose of use.
  • In one embodiment, the vector is a viral vector. Viral vectors, particularly those used in gene therapy applications, are well known in the art. Such viruses may be RNA and DNA viruses with either single-stranded (ss) or double-stranded (ds) genomes. For example, viral vectors include, but are not limited to, adenoviruses, adeno-associated viruses (AAV), alphaviruses, flaviviruses, herpes simplex viruses (HSV), measles viruses, rhabdoviruses, retroviruses, lentiviruses, Newcastle disease virus (NDV), poxviruses and picornaviruses. Insert capacity and tropism can vary, therefore a viral vector may be chosen based upon the intended application.
  • AAV vectors are increasingly favoured as an optimal gene therapy viral vector, as these have improved safety. However, a limitation is their smaller cargo size. The SSE 4-part assemblies described herein ideally suited to AAV. Therefore, in one embodiment, the vector is an AAV. Different AAV serotypes differ in their tropism, therefore the type of AAV vector used can be chosen depending upon the type of tissue targeted. The AAV vector may be selected from a number of serotypes known in the art, for example any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11, or may be a non-natural variant. In one embodiment, the AAV is selected from: AAV1, AAV2 or AAV5.
  • According to a further aspect of the invention, there is provided a vector comprising the synthetic super-enhancer as described herein and a transgene (i.e. a payload, such as a therapeutic payload). As described herein, the synthetic super-enhancer may be operably linked to other expression elements, such as a promoter.
    • Compositions and kits
  • The present invention also relates to compositions comprising the functional nucleic acid molecules or vectors described herein. The composition may comprise components which enable delivery of said functional nucleic acid molecules by viral vectors (AAV, lentivirus and the like) and non-viral vectors (nanoparticles, lipid particles and the like).
  • According to a further aspect of the invention, there is provided a composition comprising the synthetic super-enhancer, functional nucleic acid molecule or the vector as described herein, and an acceptable carrier. Suitable carriers are known in the art, In certain embodiments, the carrier is selected based upon its ability to facilitate the transfection of a target cell with one or more functional nucleic acid molecules.
  • According to a further aspect of the invention, there is provided a composition comprising the functional nucleic acid molecule or the vector as described herein, for use in therapy.
  • According to a further aspect of the invention, there is provided a composition comprising the functional nucleic acid molecule or the vector as described herein, for use in the treatment of cancer.
  • According to a further aspect of the invention, there is provided the use of the functional nucleic acid molecule (or vector or composition) as defined herein for the manufacture of a medicament, particularly for the treatment of cancer.
  • According to a further aspect of the invention, there is provided a kit comprising the functional nucleic acid molecule as described herein, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug. Therefore, in this aspect, the kit additionally comprises the inactive prodrug (i.e. for administration with the functional nucleic acid molecule).
    • Treatment methods
  • According to a further aspect of the invention, there is provided a method for treating a disease comprising administering the functional nucleic acid molecule, the vector or the composition according as described herein, to a patient.
  • References to "subject", "patient" or "individual" refer to a subject, in particular a mammalian subject, to be treated. Mammalian subjects include humans, non-human primates, farm animals (such as cows), sports animals, or pet animals, such as dogs, cats, guinea pigs, rabbits, rats or mice. In some embodiment, the subject is a human. In alternative embodiments, the subject is a non-human mammal, such as a mouse.
  • As used herein, "treating" a disease or disorder means reducing the frequency and/or severity of at least one sign or symptom of the disease or disorder experienced by a subject.
  • In one embodiment, the disease is cancer. "Cancer," as used herein, refers to the abnormal growth or division of cells. Generally, the growth and/or life span of a cancer cell exceeds, and is not coordinated with, that of the normal cells and tissues around it. Cancers may be benign, pre-malignant or malignant. Cancers may also be primary cancers or secondary cancers. A primary cancer is the original organ or tissue where the cancer began, whereas a secondary cancer is the result of the primary cancer spreading (or metastasising) to another site in the body.
  • Cancer occurs in a variety of cells and tissues, including the oral cavity (e.g. mouth, tongue, pharynx), digestive system (e.g. oesophagus, stomach, small intestine, colon, rectum, liver, bile duct, gall bladder, pancreas), respiratory system (e.g. larynx, lung, bronchus), bones, joints, skin (e.g. basal cell, squamous cell, meningioma), breast, genital system (e.g. uterus, ovary, prostate, testis), urinary system (e.g. bladder, kidney, ureter), eye, nervous system (e.g. brain), endocrine system (e.g. thyroid), and hematopoietic system (e.g. lymphoma, myeloma, leukaemia, acute lymphocytic leukaemia, chronic lymphocytic leukaemia, acute myeloid leukaemia, chronic myeloid leukaemia).
  • In a further embodiment, the cancer is a cancer located in the brain or spinal cord (i.e. the central nervous system), such as a primary or secondary cancer located in the central nervous system. The invention finds particular use in the treatment of glioblastoma.
  • The functional nucleic acid molecule (or vector or composition) may be administered by any suitable mode of delivery for the intended treatment, such as intravenously, intraarterially, intracardially, intracutaneously, subcutaneously, interperitoneally, intramuscularly or orally. In one embodiment, the functional nucleic acid molecule, vector or composition is administered systemically. Administration may also be direct to the site of disease. Therefore, in one embodiment, the functional nucleic acid molecule, vector or composition is administered locally, e.g. directly into the organ or tissue, such as intratumorally.
  • According to a further aspect of the invention, there is provided a method for treating glioblastoma comprising administering a functional nucleic acid molecule and an inactive prodrug to a patient,
    • wherein the functional nucleic acid comprises a synthetic super-enhancer activated by a SOX transcription factor and a suicide gene which encodes a protein capable of converting the inactive prodrug into a cytotoxic drug, and
    • wherein the suicide gene is expressed upon activation of the synthetic super-enhancer by the SOX transcription factor in glioblastoma cells.
  • In one embodiment, the inactive prodrug is administered concomitantly or sequentially to the functional nucleic acid molecule.
  • It will be understood that methods of treatment will involve administration of a therapeutically effective amount. The term "therapeutically effective amount" is an amount that is effective to ameliorate or treat a symptom of a disease or disorder. A therapeutically effective amount can be a "prophylactically effective amount" as prophylaxis can be considered therapy.
  • It will be understood that the embodiments described herein may be applied to all aspects of the invention, i.e. the embodiment described for the uses may equally apply to the claimed methods and so forth.
    • CLAUSES
  • A set of clauses defining the invention and its preferred aspects is as follows:
    1. 1. A synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
    2. 2. The synthetic super-enhancer according to clause 1, wherein each of the two or more enhancer sequences within the synthetic super-enhancer are less than 300 nucleotides long, in particular 160 nucleotides long.
    3. 3. The synthetic super-enhancer according to clause 1 or clause 2, wherein the synthetic super-enhancer is less than 1200 nucleotides long, in particular less than 700 nucleotides long.
    4. 4. The synthetic super-enhancer according to any one of clauses 1 to 3, wherein the synthetic super-enhancer comprises four enhancer sequences.
    5. 5. The synthetic super-enhancer according to any one of clauses 1 to 4, wherein the transcription factor is a transcription factor of the SOX family.
    6. 6. The synthetic super-enhancer according to any one of clauses 1 to 5, wherein the synthetic super-enhancer comprises at least one SOX dimer motif.
    7. 7. The synthetic super-enhancer according to clause 6, wherein the SOX dimer motif comprises SEQ ID NO: 1.
    8. 8. The synthetic super-enhancer according to any one of clauses 1 to 5, wherein the synthetic super-enhancer comprises at least one SOX motif.
    9. 9. The synthetic super-enhancer according to clause 8, wherein the SOX motif is a SOX2 motif.
    10. 10. The synthetic super-enhancer according to clause 8 or clause 9, wherein the SOX2 motif comprises SEQ ID NO: 3.
    11. 11. The synthetic super-enhancer according to any one of clauses 1 to 10, wherein the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1.
    12. 12. The synthetic super-enhancer according to any one of clauses 1 to 11, wherein the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80.
    13. 13. The synthetic super-enhancer according to any one of clauses 1 to 12, wherein the synthetic super-enhancer additionally comprises a transcriptional regulator.
    14. 14. A functional nucleic acid molecule comprising the synthetic super-enhancer according to any one of clauses 1 to 13, operably linked to a transgene.
    15. 15. The functional nucleic acid molecule according to clause 14, wherein the transgene encodes a therapeutic payload.
    16. 16. The functional nucleic acid molecule according to clause 14, wherein the transgene encodes an adverse payload.
    17. 17. The functional nucleic acid molecule according to clause 16, wherein the adverse payload encodes a protein that stimulates an immune response that leads to the recruitment of cytotoxic immune cells.
    18. 18. The functional nucleic acid molecule according to clause 16, wherein the adverse payload encodes a cytotoxic substance.
    19. 19. The functional nucleic acid molecule according to any one of clauses 1 to 18, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug.
    20. 20. The functional nucleic acid molecule according to any one of clauses 14 to 19, wherein the synthetic super-enhancer is operably linked to a promoter.
    21. 21. A functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
    22. 22. The functional nucleic acid molecule according to clause 21, wherein the transcription factor is differentially expressed in the target aberrant cell.
    23. 23. The functional nucleic acid molecule according to clause 21 or clause 22, wherein the transcription factor is a developmental or stem-cell affiliated transcription factor.
    24. 24. The functional nucleic acid molecule according to any one of clauses 21 to 23, wherein the transcription factor is a transcription factor of the SOX family.
    25. 25. The functional nucleic acid molecule according to any one of clauses 21 to 24, which is activated by SOX2.
    26. 26. The functional nucleic acid molecule according to any one of clauses 21 to 25, wherein the synthetic super-enhancer comprises at least one SOX dimer motif.
    27. 27. The functional nucleic acid molecule according to clause 26, wherein the SOX dimer motif comprises SEQ ID NO: 1.
    28. 28. The functional nucleic acid molecule according to any one of clauses 21 to 25, wherein the synthetic super-enhancer comprises at least one SOX motif.
    29. 29. The functional nucleic acid molecule according to clause 28, wherein the SOX motif is a SOX2 motif.
    30. 30. The functional nucleic acid molecule according to clause 28 or clause 29, wherein the SOX2 motif comprises SEQ ID NO: 3.
    31. 31. The functional nucleic acid molecule according to any one of clauses 21 to 30, wherein the synthetic super-enhancer comprises two or more enhancer sequences.
    32. 32. The functional nucleic acid molecule according to any one of clauses 21 to 31, wherein the synthetic super-enhancer comprises four enhancer sequences.
    33. 33. The functional nucleic acid molecule according to clause 31 or clause 32, wherein each of the two or more enhancer sequences has a different sequence.
    34. 34. The functional nucleic acid molecule according to any one of clauses 31 to 33, wherein each of the two or more enhancer sequences is derived from different genomic loci.
    35. 35. The functional nucleic acid molecule according to any one of clauses 31 to 34, wherein each of the two or more enhancer sequences within the synthetic super-enhancer are less than 300 nucleotides long, in particular about 160 nucleotides long.
    36. 36. The functional nucleic acid molecule according to any one of clauses 31 to 35, wherein each of the two or more enhancer sequences within the synthetic super-enhancer comprise a sequence selected from: a SOX motif and/or SOX dimer motif.
    37. 37. The functional nucleic acid molecule according to any one of clauses 21 to 36, wherein the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1.
    38. 38. The functional nucleic acid molecule according to any one of clauses 21 to 37, wherein the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80.
    39. 39. The functional nucleic acid according to any one of clauses 21 to 38, wherein the synthetic super-enhancer is operably linked to a promoter.
    40. 40. The functional nucleic acid molecule according to any one of clauses 21 to 39, wherein the adverse payload encodes a protein that stimulates an immune response that leads to the recruitment of cytotoxic immune cells.
    41. 41. The functional nucleic acid molecule according to any one of clauses 21 to 39, wherein the adverse payload encodes a cytotoxic substance.
    42. 42. The functional nucleic acid molecule according to any one of clauses 1 to 41, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug.
    43. 43. The functional nucleic acid molecule according to clause 42, wherein the suicide gene is a herpes simplex virus thymidine kinase (HSV-TK) gene and the prodrug is ganciclovir, acyclovir or valacyclovir.
    44. 44. The functional nucleic acid molecule according to any one of clauses 21 to 43, wherein the aberrant cell is a cancer cell or a neoplastic cell and the adverse payload is an anti-cancer payload.
    45. 45. The functional nucleic acid molecule according to any one of clauses 21 to 44, wherein the aberrant cell is a glioblastoma stem cell.
    46. 46. A synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif.
    47. 47. The synthetic super-enhancer according to clause 46, wherein each of the two or more enhancer sequences has a different sequence.
    48. 48. The synthetic super-enhancer according to clause 46 or clause 47, wherein each of the two or more enhancer sequences is derived from different genomic loci.
    49. 49. The synthetic super-enhancer according to any one of clauses 46 to 48, wherein the synthetic super-enhancer comprises four enhancer sequences.
    50. 50. The synthetic super-enhancer according to any one of clauses 46 to 49, wherein each of the two or more enhancer sequences within the synthetic super-enhancer are less than 300 nucleotides long, in particular 160 nucleotides long.
    51. 51. The synthetic super-enhancer according to any one of clauses 46 to 50, wherein each of the two or more enhancer sequences within the synthetic super-enhancer comprise a sequence selected from: a SOX motif and/or SOX dimer motif.
    52. 52. The synthetic super-enhancer according to any one of clauses 46 to 51, which is activated by SOX2.
    53. 53. The synthetic super-enhancer according to clause 52, wherein the SOX dimer motif comprises SEQ ID NO: 1.
    54. 54. The synthetic super-enhancer according to any one of clauses 46 to 51, wherein the SOX motif is a SOX2 motif.
    55. 55. The synthetic super-enhancer according to clause 54, wherein the SOX2 motif comprises SEQ ID NO: 3.
    56. 56. The synthetic super-enhancer according to any one of clauses 46 to 55, wherein the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1.
    57. 57. The synthetic super-enhancer according to any one of clauses 46 to 56, wherein the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80.
    58. 58. A synthetic super-enhancer activated by SOX2, wherein the synthetic super-enhancer comprises four enhancer sequences derived from different genomic loci and wherein each of the enhancer sequences comprises at least one SOX dimer motif.
    59. 59. A vector comprising the synthetic super-enhancer according to any one of clauses 1 to 13 or 46-58, or the functional nucleic acid molecule according to any one of clauses 14 to 45.
    60. 60. The vector according to clause 59, wherein the vector is a viral vector.
    61. 61. The vector according to clause 59 or clause 60, wherein the vector is an adeno-associated virus (AAV).
    62. 62. A composition comprising the synthetic super-enhancer according to any one of clauses 1 to 13 or 46-58, the functional nucleic acid molecule according to any one of clauses 14 to 45 or the vector according to any one of clauses 59 to 61, and an acceptable carrier.
    63. 63. A composition comprising the functional nucleic acid molecule according to any one of clauses 14 to 45, for use in therapy.
    64. 64. A composition comprising the functional nucleic acid molecule according to any one of clauses 14 to 45, for use in the treatment of cancer.
    65. 65. A kit comprising the functional nucleic acid molecule according to any one of clauses 21 to 45, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug, and the kit additionally comprises said inactive prodrug for administration with the functional nucleic acid molecule.
    66. 66. A method for treating cancer comprising administering the functional nucleic acid molecule according to any one of clauses 14 to 45 or the composition according to clauses 63 or 64, to a patient.
    67. 67. The method according to clause 66, wherein the cancer is a brain cancer, such as glioblastoma.
    68. 68. The method according to clause 66 or clause 67, wherein the functional nucleic acid molecule or composition is administered systemically.
    69. 69. The method according to clause 66 or clause 67, wherein the functional nucleic acid molecule or composition is administered locally.
    70. 70. A method for treating glioblastoma comprising administering a functional nucleic acid molecule and an inactive prodrug to a patient,
      wherein the functional nucleic acid comprises a synthetic super-enhancer activated by a SOX transcription factor and a suicide gene which encodes a protein capable of converting the inactive prodrug into a cytotoxic drug, and
      wherein the suicide gene is expressed upon activation of the synthetic super-enhancer by the SOX transcription factor in glioblastoma cells.
    71. 71. The method according to clause 70, wherein the inactive prodrug is administered concomitantly or sequentially to the functional nucleic acid molecule.
  • The invention will now be illustrated with reference to the following non-limiting examples.
    • EXAMPLES MATERIALS AND METHODS Destination vector cloning
  • In order to ensure high cloning efficiencies for both enhancer cloning and super-enhancer assembly, we built a new custom destination vector to enable efficient golden gate cloning. This also reduced reaction setup times/costs. This destination vector design encompassed: the reporter gene cassette Nanoluc-Ires-mNGreen-pA and a minimal CMV promoter (mCMV). The bacterial suicide ccdB cassette was used, for selection and efficient cloning. CDV2, contained a ccdB cassette spanning the positions enabled assembly of up to four enhancers and spacers. In contrast to CDV1, CDV2 also contains PiggyBactransposase recognition sites flanking the whole cassette. We used a Gibson assembly to generate a scar free custom destination vector (Gibson et al. 2009).
    • Bioinformatics to design of a SOX2 enhancer oligonucleotide pool
  • Suva and colleagues published technical replicates for one cell line for SOX2 binding in GSC (SOX2r1 and SOX2r2 in the MGG8 cell line, pro-neural subtype) and H3K27ac in three cell lines MGG4 (pro-neural subtype), MGG6 (classical subtype), and MGG8 (Suva et al. 2014). They also include data for the differentiated MGG8 cell (referred to here as differentiated glioma cell (DGC)). For clarity, due to their tumorigenic properties, GSC lines are also referred to as tumour-propagating cells, in contrast to DGCs (which are derived here from GSCs via addition of serum which stimulates astrocytic differentiation).
  • To determine GSC-specific SOX2 peaks, GSC SOX2r1 and SOX2r2 were overlapped with DGC SOX2_H3K27ac (a H3K27ac Chip-Seq in an SOX2 overexpressing DGCs). Additionally, shared H3K27ac peaks were also identified between the GSC cell lines to define putative enhancer sequences. These shared peaks were individually overlapped with GSC specific SOX2r1 and GSC specific SOX2r2. This safeguarded against the loss of any potentially important regions. The resulting shared peaks were then combined into one file and peaks closer than 100 base pairs (bp) were merged which also removed duplicates. The length of the peaks ranged from 15 - 5300 bp with an average length of 411 bp. Next, the pool was manually curated to remove repetitive sequences and non-enhancer sequences, such as centromeres. This resulted in a curated preliminary pool comprised of 1721 peaks ranging from 15 - 3366 bp and an average length of 402 bp.
  • To avoid PCR biases towards small fragments we also discarded all regions smaller than 100 bp resulting in 1710 peaks ranging from 115 - 3366 bp and an average length of 404 bp. These peaks were then split into 160 bp fragments. Any fragments smaller than 100 bp were again removed to avoid PCR bias. 20 bp adapters were attached on each side.
    • Cell lines
  • GSCs were derived using NSC culture conditions previously reported by Pollard et al. Briefly, cells were expanded in serum and feeder free conditions in a neural basal media with N2 and B27 supplements. Cells were grown adherently by supplementing the culture media with Laminin-1. GSC7 has been characterised by Stricker et al. HEK293 cells were obtained from the ATCC cell bank. All other GSC lines and huFb170 were derived in the Pollard lab (unpublished) and are being characterised as part of the Glioma Cellular Genetics Resource (www.gcgr.org.uk).
    • Construction of an arrayed plasmid library of enhancers
  • We chose an arrayed library format, with 160 bp enhancer fragments individually cloned into separate plasmids and arrayed in 96 well plates. These 160 bp were synthesized as a single pool of oligos, then randomly cloned into the plasmid and isolated. 20 bp x 2 were needed for PCR amplification of the pool and so a library of 200 bp fragments was synthesized (Twist Biosciences). To meet our oligo synthesis strategy, ChIP-seq peaks expressed by GSCs were merged into a single oligo. This oligonucleotide pool was PCR-amplified (using limited cycles to reduce bias and 'jackpot' products meaning products which are easier to amplify will overtake the oligonucleotide pool) and cloned into the expression vector by an efficient Golden Gate reaction. 4579 individual plasmids were then randomly picked, isolated and plated as an arrayed plasmid DNA library on 96 well plates (x48). The bacterial colony picking and production of plasmid minipreps were supported by the Edinburgh Genome Foundry (S. Rosser). This library was then screened using the optimised Nanoglo DLR assay (Nano-Glo Dual-Luciferase Reporter Assay, Promega) in 384 well format. Each plate was transiently transfected together with PGK-FFLuc in a 1:10 ratio into GSC7 cells. 2 days later a Nanoglo DLR assay was performed and assayed on a plate reader.
    • PCR amplification and clean-up for library production
  • We developed a very high efficiency of library amplification and plasmid cloning, to avoid inappropriate products, empty sequences and redundancy of the library by using a golden gate cloning and selection against the empty vector. PCR conditions were optimised to amplify the oligonucleotide pool with limited/no background and without amplification biases.
  • We used KAPA HiFi Hotstart Polymerase with GC buffer (Roche, KK2501) with 68°C annealing temperature and 5s extension time at 72°C. The oligonucleotide pool was first amplified for 10 cycles with 0.25 µl (2.5 ng input) and 0.5 µl of this reaction were used for the following 15 cycle amplification, in order to reduce PCR bias.
  • A magnetic bead-based Solid Phase Reversible Immobilization (SPRI) purification was used to minimise loss and clean up the DNA prior to golden gate cloning. Sanger sequencing of all inserts confirmed that they are diverse, and all sequences could be mapped back to a fragment of the pool and contained an adapter.
    • Screening platform for 384 well plates
  • Cells were seeded in 384 well plates using a multidrop and transfected the following day using the CyBio Felix. Two days later the experiment was terminated with a Nanoglo DLR assay and all hits with a fold change to mCMV greater than 10 were Sanger sequenced and mapped back to the genome.
    • Genomic features of validated enhancers
  • GREAT, an online tool, defines a basal regulatory domain for each gene as 1 kb downstream and 5 kb upstream of the transcription start site (TSS), meaning close genes are part of the same regulatory domain. To account for distal regulatory events, the basal gene regulatory domain is extended towards the nearest basal upstream and downstream regulatory domain within 1000 kb. GREAT then uses ontology of gene annotations and query sequences together with a binomial test to test for enrichment of gene ontology to predict the target gene (Mclean et al. 2010). We investigated the expression patterns in human adult tissues of the predicted target genes (https://gtexportal.org/home/).
    • Oligonucleotide pull down and mass spectrometry
  • The oligo was PCR-amplified using biotinylated primers. The PCR product was then SPRI purified to remove biotinylated primer dimers. These dsDNA fragments were incubated with nuclear extract from GSC7 and GSC328. They were then bound to streptavidin magnetic beads, washed three times and the frozen beads were sent for mass spectrometry analysis.
    • Cell culture procedures
  • Cell lines were cultured at 37°C in 5% CO2. Cells were grown on uncoated cell culture plastic dishes. Glioblastoma stem cell lines were grown under serum free condition using previously reported conditions (Pollard et al., 2009). For passaging cell lines were rinsed with PBS and detached using Accutase for GSC or 0.5% Trypsin/EDTA for huFb170 and HEK293, respectively. Cells were taken up in wash media and spun down at 300 xg for 3 min. They were resuspended in their respective growth media and replated. For cryo-preservation cells were resuspended in their growth media supplemented with 10% DMSO and stored at -80°C for short-term storage. For long-term preservation vials were transferred to liquid nitrogen containers.
    • Transfection of GSC, huFb170 and HEK293 cells
  • Cells were seeded at the required density. The following day the transfection was carried out. For this the Plus reagent and Lipofectamine LTX (Life Technologies, 15338030) were each diluted in half the volume of Opti-MEM I Reduced-Serum Medium (further referred to as Optimem) (Life Technologies, 31985062). Following this step, the Plus reagent/Optimem premix was added to all DNA samples followed by the Lipofectamine LTX/Optimem premix. The transfection mix was incubated for 5 min at room temperature and then carefully dropped on the cells. Generally, no media change was carried out. Cells were analysed two days following transfection.
  • HEK293 cells were seeded at the specified density in the respective plate format. The next day GMEM, DNA and PEI (homemade) are mixed and incubated for 15 min at room temperature to allow for complex formation. The transfection mix is subsequently dropped on the cells and analysis was carried out two days later.
    • Nano-Glo Dual-Luciferase Reporter Assay System (Promega)
  • This assay consists of two steps. The transfection was carried out using a normalisation plasmid PGK-Firefly-Luciferase (Promega, E5011) that was transfected in a 1/10 ratio with the plasmid of interest. First, the Firefly Luciferase activity is measured which allows to normalise to transfection efficiency. In a second step, the activity of Nanoluc is determined which is the readout of the plasmid of interest. Cells were washed 3x with PBS and 20 µl was left in the 96 well plate after the final wash (25 µl in 384 well). Oneglo buffer was added and the plate was shaken for 5 min at 480 rpm to allow cell lysis. 20 µl cell lysate in 96 well format or 25 µl cell lysate in 384 well format was then transferred into the corresponding opaque white plate and luminescence was measured at for 0.1 s per well using the Ensight Multimode Plate Reader. For the following Nanoluc reaction in a 96 well format 2 µl cell lysate was transferred into an opaque white plate containing 40 µl PBS, and 20 µl Stopglo buffer, supplemented with substrate, was added to each well. In a 384 well format 20 µl Stopglo buffer containing substrate were added on top of the undiluted cell lysate. The plate was shaken again for 5 min at 480 rpm to quench the firefly luciferase reaction and ensure good mixing. Nanoluc activity was measured for 0.1 s per well, again using Ensight Multimode Plate Reader.
  • Data obtained by the Nanoluc reaction was normalised to Firefly reaction to account for well-to-well variability of transfection efficiency. Normalised data were used to calculate the fold change to the empty vector control mCMV.
    • Immunocytochemistry
  • Cells were washed twice with PBS and fixed in 4% PFA for 10 min. Cells were permeabilised with 0.1% Triton-100 in PBS (further referred to as PBST). They were blocked with blocking solution (1% BSA in PBST with 3% goat serum) and incubated with the primary antibody at 4°C overnight (Table 3). The next day cells were washed 3x in PBST and the respective secondary antibody was applied in blocking solution and incubated for 45-60 min at room temperature. Cells were washed with PBS and incubated for 5 min with a DAPI nuclear counterstain at 1 µg/ml final concentration. Images were acquired using the Nikon TiE Microscope and NIS elements software (Nikon). Table 3: List of antibodies used in immunohistochemistry experiments
    Antibody Dilution Supplier/Catalogue number
    Primary antibodies
    Anti-SOX2 (rabbit) 1:200 Abcam (Ab92494)
    Anti-SOX2 (goat) 1:200 R&D Systems (af2018)
    Anti-Olig2 (rabbit) 1:200 Sigma (Ab9610)
    Anti-Nestin (mouse) 1:500 R&D Systems (mab1259)
    Anti-GFAP (mouse) 1:500 Millipore (ab5541)
    Anti-SOX9 (rabbit) 1:200 Millipore (ab5535)
    Anti-V5 (mouse IgG2b) 1:1000 eBioscience (14679682)
    Secondary antibodies
    Anti-rabbit (goat) - Alexa 488 fluorophore 1:1000 Invitrogen (A11008)
    Anti-rabbit (goat) - Alexa 594 fluorophore 1:1000 Invitrogen (A11012)
    Anti-goat (donkey) - Alexa 488 fluorophore 1:1000 Invitrogen (A11055)
    Anti-mouse (goat) - Alexa 594 fluorophore 1:1000 Invitrogen (A21044)
    • Flow cytometry
  • For flow cytometry, cells were detached, pelleted and resuspended in an appropriate volume of flow cytometry buffer (1% BSA in PBS, v/v). Cells were stained with Draq7 (Abcam, ab109202, f.c. 0.1 µM) as a live/dead stain and analysed using the BD LSRFortessa cell analyser (4 lasers, BD Bioscience). Analysis of flow cytometry data was carried out in the FlowJo Analysis software (FlowJo, version 10.6.2).
    • Quantitative Real-time polymerase chain reaction (qRT-PCR)
  • For qRT-PCR the TaqMan Universal PCR Master Mix (Applied Biosystems) and the TaqMan gene expression assays (Life Technologies) were used on a Quant Studio7 Flex Real-Time qPCR machine. RNA samples which did not undergo reverse transcription to assess DNA contamination and water controls were employed on every plate. Additionally, qRT-PCR was carried out in technical duplicates. Data analysis was performed using the ddCt method which assumes 100% PCR efficiency and is guaranteed with TaqMan assays. Briefly, the mean was calculated for technical replicates and normalised to the housekeeping gene GAPDH which yields the ddCt value. These values were further normalised to a calibrator sample (GSC7) to give the ddCt.
    • Production of entry and final vector with the Extensible Modular Mammalian Assembly (EMMA) Toolkit
  • Vectors were designed and produced according to Martella et al. 2017. Briefly, for the domestication of a new part, BsaI and BsmBI sites were removed. The new part was PCR amplified using primers generating an overhang for the fusion sites and BsaI site. This ensured simple and efficient cloning into the part entry vector. All part entry vectors contain a red fluorescent protein (RFP) which is recombined with the to be cloned part, thus, increasing the cloning efficiency as only white colonies can contain the part. To assemble an expression vectors, all parts are mixed with the acceptor vector in an equimolar ratio. To increase cloning efficiency the acceptor vector contains the bacterial suicide cassette ccdB which is recombined with the part of the expression vector. Therefore, bacteria which take up the unmodified acceptor will not be able to make colonies.
    • Western blotting
  • Cells were scraped in PBS and spun down at 0.3 g twice to remove all liquid. Cell pellets were resuspended in 70 µl of RIPA buffer (50 mM Tris-HCI pH 8.0 , 150 mM NaCl, 1% NP-40, 0.5% deoxycholate, 0.1% SDS and protease inhibitor (Complete, Roche, 11697498001) and incubated for 5 min on ice. Lysates were centrifuged at 13000 rpm for 10 min at 4°C (centrifuge 5415D, Eppendorf). And the supernatant was collected in a new tube. Protein extracts were quantified using the Pierce BCA Protein Assay Kit (Thermo Scientific, Cat: 23225) according to the manufacturer's instructions.
  • 5% of the total volume of 4x Lithium dodecyl sulfate (LDS) buffer containing 50 mM DTT was added to the cellular extracts and samples were denatured at 95 °C for 10 min. Samples were loaded in 4-12% polyacrylamide gels prepared by Dr Carla Blin with a Spectra Multicolour Broad Range Protein Ladder (Thermo Scientific, Cat: 26634) or BioRad Precision Plus Protein Dual Colour standards (Cat: 1610377). Protein band transfer to a Immobilon PVDF membrane (Millipore, IPVH00010) was carried out by wet electroblotting or semi-dry blotting using the Biorad Trans-blot turbo system following manufacturer instructions. 5% milk in TBS-T (TBS + 0.1% Tween-20) was used for membrane blocking for 1 hour at room temperature, followed by primary antibody incubation in 5% milk in TBS-T while rocking overnight (Table 4). The next morning, the membrane was washed three times with 5 min washed at room temperature in TBS-T and incubated with secondary antibody coupled to horseradish peroxidase in 5% milk in TBS-T at room temperature for 1 hour (Table 4). Again, the membrane was washed three times for 5 min in TBS-T and developed using homemade enhanced chemiluminescence (ECL) solution or Clarity ECL Western Blotting substrate (Bio-Rad, Cat:170-5061) and imaged using X ray films or a Bio-Rad ChemiDoc™ Imager. Table 4: List of antibodies used in western blotting experiments
    Antibody Dilution Supplier/Catalogue number
    Primary antibodies
    Anti-SOX2 (rabbit) 1:1000 Abcam (ab92494)
    Anti-SOX9 (rabbit) 1:500 Millipore (ab5535)
    Anti-GAPDH (mouse) 1:10000 Ambion (AM4300)
    Secondary antibodies
    Anti-rabbit 1:5000 Novex (A16110)
    Anti- mouse 1:5000 Novex (A16027)
    • Nuclear extracts
  • All the buffers were prepared the day before, passed through a 22 µm filter (except the dialysis buffer) and left at 4°C overnight. DTT and protease inhibitors were added just before use. The cells were scraped on the media and collected on 50 ml falcons, which were spun at 1350 rcf 5 minutes at 4°C. The pellet was resuspended in 50 ml of ice cold PBS, an aliquot was taken for cell counting, and spun again spun at 1350 rcf 5 minutes at 4°C. The pellet was then resuspended in 5 ml per 40 million cells of ice cold buffer A (10 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCI, 0.5 mM DTT, protease inhibitors (Complete, Roche, 11697498001)) and incubated on ice for 10 min. The cell suspension was transferred to a glass Dounce homogenizer and dounced 40 times on ice. The cell suspension was transferred to a falcon and centrifuged at 1350 rcf for 10 min at 4°C. The supernatant was discarded (cytosolic extract) and the pellet resuspended in 100 µl per 10 million cells in ice cold buffer B (20 mM HEPES pH 7.9, 5% glycerol, 1M NaCl, 1.5 mM MgCI2, 0.2 mM EDTA pH 8.0, 0.5 mM DTT, protease inhibitors (Complete, Roche, 11697498001)). The suspension was rotated for 30 minutes at 4°C and transferred into a dialysis membrane (SnakeSkin, Thermo Scientific, Cat 68100). Dialysis was carried out in 500 ml of dialysis buffer (20 mM HEPES pH 7.9, 5% glycerol, 100 mM KCI, 0.83 mM EDTA pH 8.0, 1.66 mM DTT, protease inhibitors (Complete, Roche, 11697498001)) for two hours at 4°C with rotation. Dialysis buffer was changed (500 ml) and the dialysis was continued overnight at 4°C. The extract was collected in an 1.5 ml tube and spun at maximum speed for 15 min at 4°C (centrifuge 5415D Eppendorf). The supernatant was collected into new 1.5 ml tubes and quantified (Pierce BCA Protein Assay Kit, Thermo Scientific, Cat 23225). 100 µg aliquots were flash frozen in liquid nitrogen and stored at -80°C.
    • PCR amplification with biotinylated primers and purification
  • Enhancers were amplified with 5' biotinylated primers (Table 5) using PrimeStar Max (Takara) according to the manufacturer's instructions. Table 5: 5' Biotinylated primers for transcription factor pull down
    Primer number Sequence SEQ ID NO.
    Forward primer 595 TGATCCGTCTCgCCCTactaggttactggtgcatgc 81
    Reverse primer 596 ACTAACGTCTCgGAGCacccaaactattggagcgag 82
  • PCR purification using Agencourt AMPure XP magnetic beads (Beckman Coulter) was carried out according to the manufacturer's instructions. PCR product quantification using Tapestation and reagents was carried out according to manufacturer's instructions.
    • Precipitation of interacting proteins
  • Streptavidin Magnetic Bead (NEB, S1420S) were used according to the manufacturer's instructions. Briefly, 10 µl beads were aliquoted into LoBind tubes and washed three times with binding buffer (20 mM Tris-HCI pH 7.5, 0.5 M NaCl, 1 mM EDTA) on the magnetic stand. 20 µl biotinylated DNA (∼ 20 pmol) were mixed with 200 µl binding buffer and was added to the beads. The suspension was rotated at room temperature for 2 hours. The beads were washed again three times with binding buffer and 50 µg nuclear extract was added (total volume 50 µl). Beads, DNA and nuclear extract, to which 150 µl dialysis buffer (20mM HEPES pH 7.9, 5% glycerol, 100 mM KCI, 0.83 mM EDTA pH 8.0, 1.66 mM DTT, protease inhibitors (Complete, Roche, 11697498001)) was added, were rotated overnight at 4°C. The following morning, beads were washed three times with wash buffer (20mM HEPES pH 7.9, 5% glycerol, 250 mM NaCl, 0.83 mM EDTA pH 8.0, 1.66 mM DTT). For western blotting, proteins were eluted in 20 µl loading buffer (lithium dodecyl sulfate (LDS) buffer containing 50 mM DTT) and boiled for 5 min to denature the proteins. For mass spectrometry beads were sent dry to the facility.
    • Zebrafish experiments
  • All embryos are obtained by natural spawning and collected in conditioned aquarium water in 0.00001% methylene blue. Embryos were treated with 200 µM N-phenylthiourea (PTU) (Sigma) from 6-hours post fertilisation (hpf) for the duration of the experiment to inhibit pigmentation (Karlsson, Von Hofsten, and Olsson 2001).
  • Zygotes were injected at the one-cell stage of development. Eggs were kept in 1.5% Agarose (Sigma) moulds as described by Nusslein-Volhard and Dahm 2002 for microinjection. Microinjection needles were pulled from glass capillaries (Harvard Apparatus, USA) using the P-97 Flaming/Brown Micropipette Puller (Sutter Instruments, USA). Needle pull parameters are as follows: Heat: 550; Pull: 200; Velocity: 55; Time: 150. Microinjection was performed on the PV820 Pneumatic PicoPump (World Precision Instruments [WPI], USA) system. DNA constructs were created using the Tol2Kit system (Kawakami 2007, Kwan et al. 2007). Approximately 2 nL of plasmid DNA (30 ng/µL) containing Tol2 capped mRNA (20 ng/µL), supplemented with 0.2% w/v phenol red (Sigma) to facilitate visualization of injected volume, were injected. Embryos were imaged at 24-48 hpf on a wide-field fluorescent microscope live following anaesthesia with Tricaine.
    • Adeno-associated virus (AAV) transduction assay
  • HEK293 cells are seeded the day before the transfection into a 6 well plates so that on the day of transfection confluence would be at 60-70%. Before HEK293 cells are transfected with PEI a media change is carried out as this media will be conditioned with virus over the for two days. The following days HEK293 or GSC7 cells are seeded at low density (10-20%) in the same or a smaller plate format (6 or 12 well plate). AAV-conditioned media is spun down at 1300 rpm for 4 min to remove contaminating cells and the supernatant is transferred to the HEK293 cells seeded at low density. Cells are analysed on the microscope or flow cytometry.
    • Cell seeding and transduction for killing assays
  • On the day of cell seeding, cells were detached using above described method. Cells were counted using hemocytometer and seeded into either 96- (1,000 cells per well in 50µL), 24-(30,000 cells per well in 500µL) or 6-well (60,000 cells per well in 2mL) Corning plate and placed into incubator at 37°C/ 5% CO2. The next day, AAV virus stocks were thawed at room temperature and an appropriate amount of virus stock was added to required amount of culture media to achieve final multiplicity of infection (MOI) of 5 x 105. Culture media containing viral particles was added to cells without replacement of existing media. Cells were returned to 37°C/5% CO2.
    • Drug treatment
  • Lyophilised GCV was diluted in DMSO to achieve 100mM stock concentration. GCV stocks were aliquoted and were stored at -20°C for no longer than 1 month. To make a working stock concentration, GCV was diluted 1:100 in appropriate culture media and then 20 µL of such working stock was added to wells already containing 80 µL of culture media (achieving another 1:5 dilution). Final concentration of GCV on cells was 200 µM).
  • As negative control, DMSO was diluted 1:100 in appropriate culture media to achieve working stock. 20 µL of working stock was added to wells already containing 80 µL culture media. As positive control, 20 µL of DMSO was added to wells with 80 µL of culture media, achieving final concentration of 20% DMSO.
    • Incucyte Live-cell imaging
  • To track cell proliferation and morphological changes during treatments, cells were monitored using the Incucyte live-cell imaging system. Whole well imaging of Corning 96 well-plate every 4 hours. Basic confluence scoring analysis software (Incucyte) was used to estimate confluence. Images at specific time points were extracted to verify cell confluence and morphology.
    • MTT assay
  • On the day of assay culture media was replaced with 0.3mg/mL MTT solution (diluted in cell line-appropriate culture media). Cells were placed in incubator at 37°C/5% CO2 for 3 hours. After incubation, media was removed and 70 µL of DMSO is added to each well. Each plate was kept in the dark at 37°C for 20 minutes, shaking it occasionally. Before reading the plate, each well was visually inspected to make sure that all (formazan) crystals were dissolved. Plate was read with plate reader at 560nm absorbance.
    • Data analysis
  • Most data analysis was carried out using Microsoft Excel Version 16.23 for Mac and GraphPad Prism 7. Error bars are shown as the standard deviation of the mean. Some data analysis was carried out using RStudio version 1.1.456 (RStudio Team 2015). For generating illustration biorender.com and Adobe Illustrator 22.0.1 were used. Furthermore, open-source programmes were used, such as bedtools (Quinlan and Hall 2010), GREAT (Mclean et al. 2010), fastasplitter (Stothard 2000) and MEME (Bailey et al. 2009) for various analyses.
    • EXAMPLE 1 - Identification of functional SOX2 enhancers
  • To first establish proof of concept as to whether synergistic activity could be achieved when combining individually active enhancers into clustered multi-part arrays we first identified a small set of candidate enhancers. These were selected based on the proximal gene having a known role in neural stem cell (NSC) self-renewal (POU3F2, POU3F3, CHD7, ASCL1, SOX6, ETV1) as well as using available differential expression data for NSCs versus primary human fibroblasts. Five SOX2 candidate autoregulatory enhancers were also included. These enhancers (typically ∼500-800bp) were cloned into plasmid expression vectors harbouring mNeonGreen and a Luciferase reporter cassette and tested for their individual enhancer activity using two independent patient-derived glioblastoma stem cell (GSC) cell lines (G7 and G328) (Figure 1). Six of these enhancers were functional with more than 10-fold increased expression of NanoLuc over mCMV (254, 270, 282, 292, 312 and 316; range from 10-300 fold). None of these were active in HEK293 cells (negative control). Table 6: Predicted target genes and distance from enhancer fragment to transcription start site (TSS)
    Enhancer hg19 Gene 1 Distance to TSS1 for Gene 1 Gene 2 Distance to TSS2 for Gene 2
    252 chr8:61788019-61789039 CLVS1 -411985 CHD7 197192
    254 chr7:14060491-14061192 ETV1 -31271 DGKB 882144
    270 chr9:109363039-109363802 ZNF462 -261957 TMEM38B 906596
    282 chr3:181101249-181102012 DNAJC19 -394070 SOX2 -328091
    284 chr3:180970481-180971050 SOX2 -458956 DNAJC19 -263205
    286 chr3:180971430-180972034 SOX2 -457990 DNAJC19 -264171
    292 chr3:182010198-182010810 ATP11 B -500784 SOX2 580782
    294 chr3:182023544-182024242 ATP11 B -487395 SOX2 594171
    310 chr12:103359143-103359469 STAB2 -621745 ASCL1 7842
    312 chr11:16169685-16170249 SOX6 327968 - -
    316 chr11:16213249-16214048 SOX6 284286 - -
    324 chr6:99195817-99196383 POU3F2 -86480 - -
    336 chr2:105475793-105477403 MRPS9 -177843 POU3F3 4629
    • EXAMPLE 2 - Assembly of four different enhancers results in synergistic increases in transcriptional activity
  • In order to investigate whether combining multiple enhancers can increase activity we first built versions concatemers of either two enhancers (2x), four enhancers (4x) or eight enhancers (8x) (concatemers) (i.e. multiple copies of the same enhancer). We chose three different individual enhancers with variable strength: 270 (about 100-fold), 254 (about 20-fold), and 312 (about 10-fold). For 270, in both 2-part and 4-part enhancers, we noted only modest synergistic effects compared to the individual enhancer activity. The 4-part enhancer resulted in about 500-fold activity (Figure 1F), compared to about 100-fold for the individual enhancer. Surprisingly, we observed no additional gain by increasing the copies to an 8-part concatemer. Similar trends were observed for an independent patient line, GSC328. Only background levels of luciferase activation, comparable to the mCMV negative control, were seen in HEK293 cells for all constructs.
  • We next tested whether mixing together different enhancers from different genes would result in improved synergy (Figure 1K). We therefore combined the top 4 individual enhancers identified in G7 (270, 282, 292 and 316) into a new synthetic enhancer (termed T4). Indeed, we noted a remarkable increase with more than 5000-fold increased expression for T4 relative to mCMV (Figure 1L) using Nanoluc reporter assays (Nano-Glo Luciferase Assay and Nano-Glo Dual-Luciferase Reporter Assay, both Promega). This was further validated using flow cytometry to score mNGreen in G7 cells (Figure 1I) which indicated levels of T4 were approximately 50-60% of that observed for full length CMV in G7 cells. Combining enhancers from different genes therefore results in synergistic effects and major increases in enhancer activity in GSCs, but without increasing background expression in HEK293 cells. These cell type-specific synthetic clusters of enhancers are subsequently referred to as 'synthetic super-enhancers' (SSEs).
    • EXAMPLE 3 - Activity of the T4 synthetic super-enhancer in GSCs is reduced following astrocyte differentiation
  • We next tested whether the SSE-T4 synthetic super-enhancer was specific to the GSC state and therefore lost upon their differentiation into astrocytes where SOX2 is downregulated. G7 cells can be efficiently differentiated into an astrocyte-like cells following exposure to foetal calf serum (FCS) over a 10-15 day period. GSCs (G7) were therefore stably transfected with the SSE-T4 expression cassette (using the PiggyBac transposase system) and mNGreen+ cells sorted using fluorescence activated cell sorting (FACs). These were plated into 5% FCS the following day and mNGreen expression was measured every 5 days using flow cytometry over a 15 day time-course (Figure 1H-J). Expression of mNGreen was significantly decreased by day 5 based on live cell fluorescence imaging. This was confirmed by flow cytometry, which showed approximately 50% of cells lost mNGreen by day 5, and approximately 80% by day 15. These data indicate the SSE-T4 has high activity in GSCs, but not in their differentiated astrocyte-like progeny and thus the SSE is cell-type specific.
    • EXAMPLE 4 - Systematic screening of an arrayed plasmid library of SOX2 enhancers
  • The above data provided proof-of-principle that combining enhancers into four-part arrays can increase transcriptional activity, without compromising background expression in non-GSC cells. We reasoned that a functional screen of enhancer fragments (160bp), could be performed using the full set of candidate genome-wide SOX2 enhancers in high throughput 384-well plate based luciferase assays to systematically identify functional enhancers with optimal performance and smaller size when used in SSEs. By performing such screens in patient-derived GSCs, we can overcome the limitations of existing serum grown cancer cell lines, which do not have the appropriate identity and associated enhancers.
  • 160 bp was chosen as this provides sufficient size for nucleosome binding and is likely to be an important attribute in the evolution of the grammar within functional enhancers (Soufi et al. 2015). Moreover, 160 bp is a convenient size for synthesis of a pooled oligonucleotide library that incorporates 20 bp ends for subsequent construction of an arrayed plasmid library. We favoured an arrayed plasmid library constructed from synthetic oligonucleotides, over other pooled library screening strategies, such as STARR-seq (Muerdter et al. 2018, Arnold et al. 2013), as this ensures improved signal to noise and straightforward validation of hits.
  • We therefore designed a set of oligonucleotides that could be synthesized as a pool. We re-analysed the datasets from Suva et al. 2014, and defined a set of GSC-specific SOX2 binding peaks that overlapped with H3K27ac, which identified 1710 different enhancers. These enhancers were on average about 400 bp (range: 115-3366 bp). We split these sequences in silico into 160 bp elements that overlapped by 100 bp. 9523 different oligonucleotide sequences were then synthesized as a pool, PCR amplified, cloned into an arrayed plasmid library of 48 x 96 well plates (4579 individual plasmids in total). Sanger sequencing a subset of the resulting plasmids confirmed that the majority (-70%) of these plasmids contained an appropriate enhancer.
  • The SOX2 enhancer library was screened in 384-well format using optimised luciferase assays. 135 plasmids were identified as functional with more than 10-fold increase over mCMV. 52 of these 135 initial hits were then validated using independent Nanoglo DLR assays in triplicate (Figure 2). 16 of these 52 were found more than once. Hits were sanger-sequenced, confirmed to contain an enhancer and mapped back to the human genome with an expected fragment from the original designed set.
  • We next validated the top 17 fragments (more than 30-fold increase over mCMV) using an independent flow cytometry assay across multiple cell lines (Figure 2). These were active in an independent patient-derived GSC line (GSC328) but were inactive in non-neural cells tested (HEK293 cells and human primary fibroblasts, huFb170). We found that the majority of the top hits are evolutionarily conserved sequences across vertebrates. The top 5 enhancers were each more than 100-fold compared to mCMV (range: 100-260-fold) based on NanoLuc. These were validated by flow cytometry.
  • ID1101 is located in an intron of PRCP; ID2904 is located in the intronic region of the MYO18 gene and in proximity to SEZ6L; ID0109 is located in a gene-rich region between TPK1 and CNTNAP2; ID4328 is in the intronic region of the zinc finger transcription factor ZNF438. ID0876 is located in the intronic region of NWD2. Table 7: Predicted target genes and distance from enhancer fragment to transcription start site (TSS)
    Fragment hg19 Gene 1 Distance to TSS1 for Gene 1 Gene 2 Distance to TSS2 for Gene 2
    ID1101 chr11:82553160-82553319 PRCP 58265
    ID2904 chr22:26319890-26320049 SEZ6L -245631 MYO18B 181790
    ID0109 chr7:145217558-145217717 TPK1 -684464 CNTNAP2 -595843
    ID4328 chr10:31308050-31308209 LYZL2 -389438 ZNF438 12737
    ID0876 chr4:37394656-37394815 RELL1 293256
    ID2339 chr8:1845248-1845407 MYOM2 -147864 ARHGEF10 73149
    ID1737 chr15:38880930-38881 068 THBS1 -992325 RASGRP1 -23962
    ID0663 chr9:109338243-109338365 ZNF462 -287134 TMEM38B 881419
    ID2706 chr2:208637297-208637434 FZD5 -3078
    ID3547 chr16:27730146-27730305 KIAA0556 168738 GSG1L 344619
  • Thus, our functional screening resulted in identification of many 160 bp enhancer fragments that have significantly improved activity compared to full-length enhancers (described above), despite being 4 to 5 times smaller in size.
    • EXAMPLE 5 - Creation of strong and selective synthetic super enhancers using newly identified SOX2 enhancers
  • We constructed synthetic super-enhancers by clustering the individually most active fragments from the screen into 4-part arrays to identify whether their strength increases synergistically while retaining cell type selectivity.
  • In order to create the strongest possible synthetic super-enhancers we designed a set of four new 4-part arrays using sequences from the Top17 enhancers. These were assembled upstream of mCMV. Fragments were ranked according to their median fold change to mCMV. The 4 most active enhancers (ID1101, ID2904, ID0109, ID4328, denoted by '1') were clustered to a 4-part array into a synthetic super-enhancer. Enhancers comprising the second group (denoted by '2') were clustered into a synthetic super-enhancer and so forth. We hypothesized that the four strongest enhancers will exhibit the highest level of expression, the next group will be second highest etc. Furthermore, by testing the synthetic super-enhancers in different cell types (GSC7, GSC328, HEK293 and huFb170) we also investigated their cell type - selectivity.
  • All four constructs tested (C1, C3, C5 and C7) induced significant and selective expression in GSC7 and GSC328 and only background expression in HEK293. No expression was detected in huFb170. Each of these synthetic super-enhancers (C1, C3, C5 and C7) exhibited a higher fluorescence intensity and a higher percentage of mNGreen+ cells than SSE-T4 (1st generation SSE discussed above), the most active synthetic super-enhancer using candidate enhancers, in GSC7 and GSC328. Remarkably, C1 and C7 induced a higher expression level than the positive control CMV, which is itself one of the strongest viral promoters. We therefore, observed clear synergistic effects of building arrays of a 4-part enhancers, resulting in extremely strong and cell type-selective synthetic super enhancers.
  • We reduced the size of the synthetic super-enhancers further by removal of the adaptors and spacers (e.g. for C1, 974 bp to 640 bp). These synthetic super-enhancers were termed SSE 1-7, as they are 7 constructs and their design follows the same rationale as C1, C3, C5, C7. All constructs showed a similar level of activity. This was comparable in levels to the full CMV, and in some cases it was higher than CMV (SSE1, 2, 3, 5 by Nanoglo DLR assay and SSE-1, 2, 3, 5, 7 by flow cytometry in GSC7. SSE-1, 2, 5 and 7 also exhibited higher intensity than CMV in GSC7. Analysis of mNGreen expression by flow cytometry was also performed for GSC328, HEK293 and huFb170. The trend is similar in GSC328. The mean fluorescence intensity (MFI) was around CMV, with SSE-6 being clearly less intense than CMV. In HEK293 cells all synthetic super-enhancers induced transcription to a similar level like mCMV. mCMV exhibited 32.5% mNGreen+ cells in comparison to non-transfected cells. SSE demonstrated small increase in expression in HEK293 compared to mCMV. The activity of SSE1-7 in huFb170 was undetectable (more than 1%). A tendency towards higher activity with smaller synthetic super-enhancers in both reporter gene assays (Nanoglo DLR assay and flow cytometry) was observed for each construct C1 vs SSE-1; C3 vs SSE-3 etc (Figure 3B, C, D). This was confirmed by live cell images (Figure 3E). Each of synthetic super-enhancers SSE-1, 3, 5 and 7 tested were similar in activity to CMV.
    • EXAMPLE 6 - Synthetic super-enhancers are less active in differentiated GSCs
  • In order to investigate the activity of SSE-2-SSE-7 under differentiating conditions, GSC7 cells were stably transfected using the Piggybac transposase system and sorted for mNGreen+ cells. A similar number of live cells was sorted for the mCMV and untransfected controls. Cells were then placed into media containing no growth factors but 5% FCS to induce astrocytic differentiation.
  • mNGreen expression was measured at 0, 1, 5, 10 and 15 days during differentiation (Figure 4E and G). We observed a drop of signal over the time course, suggesting that the synthetic super-enhancers are most highly expressed in the GSCs, and activity is decreased upon differentiation.
    • EXAMPLE 7 - Zebrafish embryos reveal highly selective, region-specific expression in forebrain
  • Zebrafish are well-suited as an experimental model to explore the tissue specificity of enhancers. We identified tissues which are shared between all constructs like ventral spinal cord expression, otic placode as well as midbrain/hindbrain and anterior forebrain. Some fragment had additional activity, such as the anterior/posterior intestine. We generally observed low expression at 24 hpf which kept increasing up to the latest measured timepoint at 48 hpf. Regarding the controls, we observed broad, unspecific expression of EGFP in the CMV control and no expression in the mCMV using the same assay (Figure 4). The mCMV control exhibited green fluorescent eyes which is probably due to spurious transcription from the Crystal eye promoter (Figure 4K).
    • EXAMPLE 8 - SSEs can be used in adeno-associated viruses to induce selective killing of GSCs
  • To test if SSEs are suitable to drive a cytotoxic payload and selectively kill GSCs, we transduced GSC7 and huFB170 cell lines with the adeno-associated virus 2 (AAV2) containing the suicide gene thymidine kinase (TK) derived from the Herpes simplex virus (HSV) in a polycistronic mRNA with the reporter gene mCherry joined by p2A. The cassettes were either driven by a constitutively active CMV promoter as a positive control (CMV_HSV-TK-v5_P2A_mCherry) or the promoter of interest, SSE-7 (SSE-7-HSV-TK-v5-P2A-mCherry). HSV-TK is a well-established prodrug which metabolises the non-cytotoxic prodrug ganciclovir (GCV) into a cytotoxic product by phosphorylation. Phosphorylated GCV competes with dGTP as a substrate for polymerase thereby leading to interference of DNA synthesis causing premature termination and cytotoxicity.
  • Flow cytometry and western blotting confirmed SSE-7 is driving both mCherry and HSV-TKv5 expression in GSC7 but not in fibroblasts (huFb170) (Figure 5). Cell confluence was recorded throughout the cytotoxicity experiment. A decrease in cell proliferation and confluence was specifically observed in cells which were transduced with CMV or SSE-7-driven TKv5-P2A-mCherry and received 200 µM GCV (Figure 6A). No significant negative effect on cell confluence was observed in cells which received virus or ganciclovir alone. MTT assay data demonstrates loss (or lack) of metabolic activity, which serves as an approximate readout for cell viability in GSC7 cells treated with CMV or SSE-7-driven TKv5-P2A-mCherry and GCV (Figure 6B). There was no statistical difference between CMV and SSE-7 (13% vs 12% viability) (p-value = 0.7792). There was a small effect of ganciclovir alone on GSC7 cell viability (89% viability). Live cell imaging confirmed these findings showing lower cell density and morphological changes linked to cellular stress, damage or death (rounded cells) after treatment (Figure 6C). In summary, both CMV and SSE-7 can drive expression of HSV-TK-v5-P2A-mCherry construct to a sufficient level in GSC7 cells to induce cell death in the presence of ganciclovir.
  • Based on live cell imaging data at the end of experiment (day 17), the majority of the huFB170 cells which were transduced with CMV-driven, but not SSE-7-driven, virus were killed (Figure 6D). This was confirmed with MTT data, demonstrating 6.3% viability in cells transduced with CMV-driven virus versus full viability in cells transduced with SSE-7-driven TKv5-P2A-mCherry (Figure 6E, n=1).
    • EXAMPLE 9 - SSEs show activity in a range of GSCs
  • It is desirable for an SSE in a proposed gene therapy to be expressed highly across diverse patient-derived glioblastoma cell lines, but inactive in other cell types. The experiment described in Example 8 was repeated in five patient-derived glioblastoma cell lines (E17, E21, E28, E31, E34). These lines were selected for this experiment as they cover a spectrum of genetic and transcription GBM subtypes and have been shown to be tumour inducing in a mouse brain. Altogether, SSE7 is active in all cell lines, but to different degrees: it is highly expressed and comparable to full-length CMV in the positive control cell line GSC7 (Figure 7C);and E17 and E28 (Figure 7C), which both belong to the classical subtype, but has a lower frequency of expression in E21, E31 and E34 (Figure 7C).
    • EXAMPLE 10 - Analysis of de novo motifs identifies a SOX dimer motif enriched in the Top 32 hits
  • We used the MEME tool, which can identify de novo motifs (Bailey et al. 2009). We used the top 32 hits as input. Unexpectedly, the significant motif that emerged was a partial palindromic SOX motif (Figure 8A). SOX2 does not form homo or heterodimers with other SOX factors; however, members of the SOXE group are well established to dimerise (SOX8, SOX9, SOX10). Interestingly, SOX9 is a well-known regulator of NSCs and GSCs, but has not been as deeply studied as SOX2 (Bulstrode et al. 2017, Huang et al. 2015, Mateo et al. 2015, and D. K. Singh et al. 2017). This motif suggested immediately that SOX2 and SOX9 might be operating at shared enhancers (Figure 8C).
  • We then investigated whether this dimer motif is a general feature of the oligonucleotide pool of sequences and mapped it to the Top 52 hits (all sequences with a 10x fold change over mCMV) compared to unconfirmed hits of the validation and in 10 random sequences of the initial oligonucleotide pool. The motif is present at high frequency in the Top 32 hits and with lower frequency in the remaining Top 33-Top 52.
    • EXAMPLE 11 - A SOX dimeric motif is essential for the activity of ID2904 in GSCs and suggests cooperation of SOX2 and SOX9 at key GSC functional enhancers
  • We next explored whether the SOX dimer was essential for enhancer function. We generated a series of variants of the motif for ID2904. The variants synthesized had: 1) decreased spacing between the half sites (-2n); 2) increased spacing between the motif half sites; 3) and 4) deletion of one half site; 5) replacement of the flanking sequences by random sequences; 6) inversion of the motif; 7) mutation of the core nucleotides; 8) replacement by the high affinity motif as reported by Jolma et al. 2013; 9) a random sequence as negative control; and 10) concatemerisation of the motif four times. These different variants enabled us to functionally dissect the key sequences within the dimer motif (Figure 8).
  • We observed an almost complete loss of activity with almost all variations of the SOX dimer motif in ID2904, confirming the importance of this dimer motif for the function of the enhancer. An exception was the altered distance between the two half-sites, which led to an increased activity. This is intriguing, as it is consistent with the notion that the spacing could be 'suboptimised' and the 2bp reduction might drive stronger binding of the SOX9 dimer (Farley et al. 2015). We conclude that the SOX dimer motif is essential for the enhancer activity of ID2904. The reduction of the spacing is also in accordance with Huang et al. 2015, who defined the optimal spacing for SOXE factor motifs.
  • Next, we aimed to confirm that indeed SOX2 and SOX9 are binding to the enhancer and the SOX dimer motif. To this end we carried out pull down assays in which the ID1101 (top hit of the screen) and ID2901 were biotinylated and incubated with nuclear extracts. Western blotting and mass spectrometry were performed to identify the key transcription factors interacting with the fragments (Figure 8). For data analysis, ID1101 was normalised to the average value of the random sequence 599 (in each cell line). The cut-off was set at two fold enrichment over 599 in both cell lines. To filter for transcription factors a list of all transcription factors was obtained from UniProt and overlapped with the detected proteins in both cell lines.
  • In coimmunoprecipitation experiments, SOX2 was pulled down specifically with ID1101 in GSC7 and GSC328, demonstrating SOX2 binding to the enhancer (Figure 8). This was confirmed in mass spectrometry as SOX2 was 23-fold enriched in GSC328 and a 4.4 fold enriched in G7, confirming the binding of this transcription factor.
  • Additionally, data described above and shown in Figure 8J demonstrates that the sequence context (grammar) surrounding the motif is functionally important as replacement of the wild-type (WT) sequence 20bp up and downstream resulted in complete loss of activity.
    • EXAMPLE 12 - A SOX dimer motif helps to filter for active enhancers in silico
  • We postulated that the presence of the motif might have the ability to increase our prediction power about which enhancer is active. To test this hypothesis, we mapped the motif to all full-length enhancers of the original SOX2 ChIP-seq datasets. 70 regions were selected for an initial screen based on their predicted target gene with a known function in GBM or neural stem cells and on clustering within the genome, meaning the regulation of the same predicted target gene. They were tested in the Nanoglo DLR assay. These were termed 'Clustered SOX dimer motif enhancers' (CSEs). Using the SOX dimer motif frequency and rational design we therefore increased the success of identifying positive enhancers around 11-fold; from -2% in the original screen (52/2610) to -22.8%, in our rational selection (16/70). Positive hits were further validated by flow cytometry in GSC7, GSC328, HEK293 and huFb170 (Figure 9).
  • An additional screen with 209 enhancers was carried out to identify further active enhancers. The enhancers were reduced to 160 bp based on their predicted motifs (termed minCSEs - see Table 1). 160 bp enhancer fragments were mixed from different target genes to cover pathways like proliferation, stemness or brain-enriched/brain-specific or glioma-enriched/glioma-specific predicted target genes based on data from the human protein atlas (https://www.proteinatlas.org/), to generate further SSEs for screening. Table 8: Verified CSE hits with genomic coordinates, predicted target gene and their distance from enhancer fragment to TSS
    Fragment hg19 Gene 1 Distance to TSS1 for Gene 1 Gene 2 Distance to TSS2 for Gene 2
    CSE012 chr11:13123591-13123982 ARNTL -175558 TEAD1 357199
    CSE005 chr1:239997099-239997375 FMN2 -257943 CHRM3 204864
    CSE034 chr17:70684065-70684473 SLC39A11 404558 SOX9 567108
    CSE078 chr7:47867049-47867394 C7orf69 32333 PKD1L1 120866
    CSE088 chr8:130645429-130646106 GSDMC 153366 - -
    CSE025 chr14:70453941-70454604 SMOC1 108140 SLC8A3 201514
    CSE033 chr17:70627702-70628067 SLC39A11 460942 SOX9 510724
    CSE014 chr11:16169648-16170321 SOX6 327950
    CSE061 chr6:118334186-118334492 PLN -535122 SLC35F1 105650
    CSE075 chr7:14543795-14544174 ETV1 -514414 DGKB 399001
    CSE054 chr5:124993695-124994093 ZNF608 -912776 GRAMD3 -701930
    CSE074 chr7:14311089-14311579 ETV1 -281763 DGKB 631652
    CSE031 chr17:70572258-70572879 SOX9 455408 SLC39A11 516258
    CSE006 chr1:61298892-61299426 C1orf87 -759717 NFIA -248375
    CSE194 chr6:99235165-99236055 POU3F2 -46970 - -
    CSE208 chr7:154534737-154535331 PAXIP1 259760 DPP6 785269
    CSE222 chr7:8421667-8422191 ICA1 -120018 NXPH1 -51656
    CSE229 chr8:82359507-82360175 PMP2 -83 - -
    • CONCLUSION
  • Mapping of transcription factor binding sites, chromatin accessibility or enhancer-associated histone marks are widely used to search for critical transcription factors (TFs) and associated enhancers. However, a major limitation is that TFs bind rather promiscuously, and the functional enhancers represent only a minor subset. We demonstrate herein that combining an array of functional enhancer sequences can lead to the formation of synthetic super-enhancers. By harnessing the natural 'grammar' of endogenous functional enhancer sequences but combining these in optimal sizes and clusters, we were able to obtain SSEs with synergistic increases of transcriptional activation without sacrificing cell type selectivity. Our data therefore support that individual enhancers can be combined to create synthetic super-enhancers that retain selectivity, yet are extremely strong at driving transcription.
    • REFERENCES
    • TABLE 1 - Sequences (without adapters) of the enhancers
    Fragment Fold change (Median) Sequence SEQ ID NO.
    ID1101 258.8
    Figure imgb0001
    		 4
    ID2904 251.6
    Figure imgb0002
    		 5
    ID0109 116.4
    Figure imgb0003
    		 6
    ID4328 100.7
    Figure imgb0004
    		 7
    ID0876 91.1
    Figure imgb0005
    		 8
    ID2339 79.6
    Figure imgb0006
    		 9
    ID1737 77.1
    Figure imgb0007
    		 10
    ID0663 59.1
    Figure imgb0008
    		 11
    ID2706 57.2
    Figure imgb0009
    		 12
    ID3547 53.2
    Figure imgb0010
    		 13
    ID0885 42.6
    Figure imgb0011
    		 14
    ID3548 40.0
    Figure imgb0012
    		 15
    ID3146 37.2
    Figure imgb0013
    		 16
    ID4310 36.3
    Figure imgb0014
    		 17
    ID4428 36.2
    Figure imgb0015
    		 18
    ID0785 34.3
    Figure imgb0016
    		 19
    ID3836 33.4
    Figure imgb0017
    		 20
    ID3765 31.7
    Figure imgb0018
    		 21
    ID1176 31.3
    Figure imgb0019
    		 22
    ID1888 31.1
    Figure imgb0020
    		 23
    ID0291 29.0
    Figure imgb0021
    		 24
    ID1244 27.8
    Figure imgb0022
    		 25
    ID0456 27.2
    Figure imgb0023
    		 26
    ID1322 26.7
    Figure imgb0024
    		 27
    ID2082 26.4
    Figure imgb0025
    		 28
    ID4035 26.2
    Figure imgb0026
    		 29
    ID1667 25.2
    Figure imgb0027
    		 30
    ID2816 25.1
    Figure imgb0028
    		 31
    ID0403-1 24.9
    Figure imgb0029
    		 32
    ID0403-2 24.9
    Figure imgb0030
    		 33
    ID4421 21.7
    Figure imgb0031
    		 34
    ID4431 21.2
    Figure imgb0032
    		 35
    ID3499 20.7
    Figure imgb0033
    		 36
    CSE194 14.54
    Figure imgb0034
    		 37
    CSE208 45.5
    Figure imgb0035
    		 38
    Figure imgb0036
    CSE222 145.9
    Figure imgb0037
    		 39
    CSE012 10.3
    Figure imgb0038
    		 40
    CSE005 11.5
    Figure imgb0039
    		 41
    CSE034 14.3
    Figure imgb0040
    		 42
    Figure imgb0041
    CSE078 10
    Figure imgb0042
    		 43
    CSE088 16.5
    Figure imgb0043
    		 44
    CSE025 21.3
    Figure imgb0044
    		 45
    Figure imgb0045
    CSE033 20.9
    Figure imgb0046
    		 46
    CSE014 27.7
    Figure imgb0047
    		 47
    CSE061 58.3
    Figure imgb0048
    		 48
    CSE075 58.1
    Figure imgb0049
    		 49
    CSE054 65.7
    Figure imgb0050
    		 50
    CSE074 250.6
    Figure imgb0051
    		 51
    Figure imgb0052
    CSE031 249.3
    Figure imgb0053
    		 52
    CSE006 524.3
    Figure imgb0054
    		 53
    minCSE031
    Figure imgb0055
    		 54
    minCSE033
    Figure imgb0056
    		 55
    minCSE034
    Figure imgb0057
    		 56
    minCSE061
    Figure imgb0058
    		 57
    minCSE074
    Figure imgb0059
    		 58
    minCSE075
    Figure imgb0060
    		 59
    minCSE194
    Figure imgb0061
    		 60
    minCSE208
    Figure imgb0062
    		 61
    minCSE222
    Figure imgb0063
    		 62
    minCSE229
    Figure imgb0064
    		 63
    Note: Fold Change refers to the expression fold change of the individual enhancer compared to mCMV.
    TABLE 2 - Sequences of full SSEs
    SSE Sequence SEQ ID NO.
    SSE-1 (ID1101_ID2904_ ID0109_ID4328)
    Figure imgb0065
    		 64
    SSE-2 (ID0109_ID4328_ ID0876_ID2339)
    Figure imgb0066
    		 65
    SSE-3 (ID0876_ID2339_ ID1737_ID0663)
    Figure imgb0067
    		 66
    SSE-4 (ID1737_ID0663_ ID2706_ID3547)
    Figure imgb0068
    		 67
    SSE-5 (ID2706_ID3547_ ID3548_ID3146)
    Figure imgb0069
    		 68
    SSE-6 (ID3548_ID3146_ ID4310_ID4428)
    Figure imgb0070
    		 69
    SSE-7 (ID4310_ID4428_ ID0785_ID3836)
    Figure imgb0071
    		 70
    SSE-8 (minCSE034_minC SE061_minCSE07 5_minCSE222)
    Figure imgb0072
    		 71
    Figure imgb0073
    SSE-9 (minCSE034_minC SE074_minCSE07 5_minCSE222)
    Figure imgb0074
    		 72
    SSE-10 (minCSE061_minC SE074_minCSE19 4_minCSE222)
    Figure imgb0075
    		 73
    SSE-11 (minCSE075_minC SE194_minCSE22 2_minCSE229)
    Figure imgb0076
    		 74
    Figure imgb0077
    SSE-12 (minCSE034_minC SE075_minCSE19 4_minCSE222)
    Figure imgb0078
    		 75
    SSE-13 (minCSE074_minC SE075_minCSE19 4_minCSE229)
    Figure imgb0079
    		 76
    SSE-14 (minCSE034_minC SE061_minCSE22 2_minCSE229)
    Figure imgb0080
    		 77
    Figure imgb0081
    SSE-15 (minCSE034_minC SE061_minCSE07 5_minCSE229)
    Figure imgb0082
    		 78
    SSE-16 (minCSE075_minC SE194_minCSE20 8_minCSE222)
    Figure imgb0083
    		 79
    SSE-17 (minCSE074_minC
    Figure imgb0084
    		 80
    SE194_minCSE22 2_minCSE229)
    Figure imgb0085
    Figure imgb0086
    Figure imgb0087
    Figure imgb0088
    Figure imgb0089
    Figure imgb0090
    Figure imgb0091
    Figure imgb0092
    Figure imgb0093
    Figure imgb0094
    Figure imgb0095
    Figure imgb0096
    Figure imgb0097
    Figure imgb0098
    Figure imgb0099
    Figure imgb0100
    Figure imgb0101
    Figure imgb0102
    Figure imgb0103
    Figure imgb0104
    Figure imgb0105
    Figure imgb0106
    Figure imgb0107
    Figure imgb0108
    Figure imgb0109
    Figure imgb0110
    Figure imgb0111
    Figure imgb0112
    Figure imgb0113
    Figure imgb0114
    Figure imgb0115
    Figure imgb0116
    Figure imgb0117

Claims (17)

  1. A synthetic super-enhancer activated by one or more transcription factors, wherein the synthetic super-enhancer comprises two or more enhancer sequences derived from different genomic loci, wherein each enhancer sequence comprises a binding site for the transcription factor and between 20 and 400 nucleotides upstream and/or downstream of the binding site for the transcription factor present in its genomic locus.
  2. The synthetic super-enhancer according to claim 1, wherein each of the two or more enhancer sequences within the synthetic super-enhancer are less than 300 nucleotides long, in particular is about 160 nucleotides long and wherein the synthetic super-enhancer is less than 1200 nucleotides long, in particular less than 700 nucleotides long.
  3. The synthetic super-enhancer according to claim 1 or claim 2, wherein the synthetic super-enhancer comprises four enhancer sequences.
  4. The synthetic super-enhancer according to any one of claims 1 to 3, wherein the synthetic super-enhancer comprises at least one SOX dimer motif and/or at least one SOX motif.
  5. The synthetic super-enhancer according to claim 4, wherein the SOX dimer motif comprises SEQ ID NO: 1.
  6. The synthetic super-enhancer according to claim 4, wherein the SOX motif comprises SEQ ID NO: 3.
  7. The synthetic super-enhancer according to any one of claims 1 to 6, wherein the synthetic super-enhancer comprises one or more enhancer sequences presented in Table 1.
  8. The synthetic super-enhancer according to any one of claims 1 to 7, wherein the synthetic super-enhancer comprises a sequence with at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 64-80.
  9. A functional nucleic acid molecule comprising the synthetic super-enhancer according to any one of claims 1 to 8, operably linked to a transgene, wherein the transgene encodes a therapeutic payload.
  10. A functional nucleic acid molecule comprising a synthetic super-enhancer activated by one or more transcription factors expressed in a target aberrant cell and an adverse payload, wherein said payload is expressed upon activation of the synthetic super-enhancer by the transcription factor(s).
  11. The functional nucleic acid molecule according to claim 10, wherein the transcription factor is differentially expressed in the target aberrant cell, and optionally wherein the transcription factor is a developmental or stem-cell affiliated transcription factor.
  12. The functional nucleic acid molecule according to claim 10 or claim 11, wherein the adverse payload encodes a protein that stimulates an immune response that leads to the recruitment of cytotoxic immune cells.
  13. The functional nucleic acid molecule according to claim 10 or claim 11, wherein the adverse payload is a suicide gene which encodes a protein capable of converting an inactive prodrug into a cytotoxic drug.
  14. A composition comprising the functional nucleic acid molecule according to any one of claims 9 to 13, for use in the treatment of cancer, such as glioblastoma.
  15. A synthetic super-enhancer activated by one or more transcription factors of the SOX family, wherein the synthetic super-enhancer comprises two or more enhancer sequences and at least one SOX motif and/or SOX dimer motif.
  16. The synthetic super-enhancer according to claim 15, wherein each of the two or more enhancer sequences has a different sequence.
  17. The synthetic super-enhancer according to claim 15 or claim 16, wherein each of the two or more enhancer sequences within the synthetic super-enhancer are less than 300 nucleotides long, in particular is about 160 nucleotides long.
EP21153875.6A 2021-01-27 2021-01-27 Functional nucleic acid molecule and method Withdrawn EP4036238A1 (en)

Priority Applications (10)

Application Number Priority Date Filing Date Title
EP21153875.6A EP4036238A1 (en) 2021-01-27 2021-01-27 Functional nucleic acid molecule and method
EP22703431.1A EP4284935A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method
KR1020237029045A KR20230137399A (en) 2021-01-27 2022-01-26 Functional nucleic acid molecules and methods
PCT/GB2022/050206 WO2022162361A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method
CN202280011408.1A CN116867901A (en) 2021-01-27 2022-01-26 Functional nucleic acid molecules and methods
JP2023544676A JP2024504412A (en) 2021-01-27 2022-01-26 Functional nucleic acid molecules and methods
BR112023014906A BR112023014906A2 (en) 2021-01-27 2022-01-26 FUNCTIONAL NUCLEIC ACID MOLECULE AND METHOD
US18/274,306 US20240092847A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method
CA3206298A CA3206298A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method
AU2022212766A AU2022212766A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
EP21153875.6A EP4036238A1 (en) 2021-01-27 2021-01-27 Functional nucleic acid molecule and method

Publications (1)

Publication Number Publication Date
EP4036238A1 true EP4036238A1 (en) 2022-08-03

Family

ID=74346875

Family Applications (2)

Application Number Title Priority Date Filing Date
EP21153875.6A Withdrawn EP4036238A1 (en) 2021-01-27 2021-01-27 Functional nucleic acid molecule and method
EP22703431.1A Pending EP4284935A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method

Family Applications After (1)

Application Number Title Priority Date Filing Date
EP22703431.1A Pending EP4284935A1 (en) 2021-01-27 2022-01-26 Functional nucleic acid molecule and method

Country Status (9)

Country Link
US (1) US20240092847A1 (en)
EP (2) EP4036238A1 (en)
JP (1) JP2024504412A (en)
KR (1) KR20230137399A (en)
CN (1) CN116867901A (en)
AU (1) AU2022212766A1 (en)
BR (1) BR112023014906A2 (en)
CA (1) CA3206298A1 (en)
WO (1) WO2022162361A1 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2024023530A1 (en) * 2022-07-29 2024-02-01 The University Court Of The University Of Edinburgh Functional nucleic acid molecule and method

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN116286991B (en) * 2023-02-10 2023-10-13 中国农业科学院农业基因组研究所 Whole genome enhancer screening system, screening method and application
WO2024230801A1 (en) * 2023-05-11 2024-11-14 Sichuan Real & Best Biotech Co., Ltd. Engineered liver-specific enhancers and their applications

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012101191A1 (en) 2011-01-25 2012-08-02 Synpromics Ltd Method for the construction of specific promoters
WO2014066848A1 (en) 2012-10-25 2014-05-01 Whitehead Institute For Biomedical Research Super-enhancers and methods of use thereof
US20140296218A1 (en) 2012-10-25 2014-10-02 Whitehead Institute For Biomedical Research Super-enhancers and methods of use thereof
WO2017155973A1 (en) 2016-03-07 2017-09-14 University Of Iowa Research Foundation Aav-mediated expression using a synthetic promoter and enhancer

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012101191A1 (en) 2011-01-25 2012-08-02 Synpromics Ltd Method for the construction of specific promoters
WO2014066848A1 (en) 2012-10-25 2014-05-01 Whitehead Institute For Biomedical Research Super-enhancers and methods of use thereof
US20140287932A1 (en) 2012-10-25 2014-09-25 Whitehead Institute For Biomedical Research Super-enhancers and methods of use thereof
US20140296218A1 (en) 2012-10-25 2014-10-02 Whitehead Institute For Biomedical Research Super-enhancers and methods of use thereof
WO2017155973A1 (en) 2016-03-07 2017-09-14 University Of Iowa Research Foundation Aav-mediated expression using a synthetic promoter and enhancer

Non-Patent Citations (32)

* Cited by examiner, † Cited by third party
Title
ARNOLD ET AL.: "Genome-wide quantitative enhancer activity maps identified by STARR-seq", SCIENCE, vol. 339, no. 6123, 2013, pages 1074 - 1077, XP002712625, DOI: 10.1126/science.1232542
BAILEY ET AL.: "MEME Suite: Tools for Motif Discovery and Searching", NUCLEIC ACIDS RESEARCH, vol. 37, 2009, pages 202 - 8
BOUMAHDI ET AL.: "SOX2 controls tumour initiation and cancer stem-cell functions in squamous-cell carcinoma", NATURE, vol. 511, no. 7508, 2014, pages 246 - 50, XP055215398, DOI: 10.1038/nature13305
BULSTRODE ET AL.: "Elevated FOXG1 and SOX2 in Glioblastoma Enforces Neural Stem Cell Identity through Transcriptional Control of Cell Cycle and Epigenetic Regulators", GENES & DEVELOPMENT, vol. 31, no. 8, 2017, pages 757 - 73
CORISHTYLER-SMITH: "Attenuation of Green Fluorescent Protein Half-Life in Mammalian Cells", PROTEIN ENGINEERING, vol. 12, no. 12, 1999, pages 1035 - 40, XP002378153
D. K. SINGH ET AL.: "Oncogenes Activate an Autonomous Transcriptional Regulatory Circuit That Drives Glioblastoma", CELL REPORTS, vol. 18, no. 4, 2017, pages 961 - 76
FARLEY ET AL.: "Suboptimization of Developmental Enhancers", SCIENCE, vol. 350, no. 6258, 2015, pages 325 - 28
GANGEMI ET AL.: "SOX2 Silencing in Glioblastoma Tumor-Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity", STEM CELLS, vol. 27, no. 1, 2009, pages 40 - 48, XP055032073, DOI: 10.1634/stemcells.2008-0493
GIBSON ET AL.: "Enzymatic Assembly of DNA Molecules up to Several Hundred Kilobases", NATURE METHODS, vol. 6, no. 5, 2009, pages 343 - 45, XP055224105, DOI: 10.1038/nmeth.1318
GUERRA-REBOLLO ET AL.: "Targeting of Replicating CD133 and OCT4/SOX2 Expressing Glioma Stem Cells Selects a Cell Population That Reinitiates Tumors upon Release of Therapeutic Pressure", SCIENTIFIC REPORTS, vol. 9, no. 1, 2019, pages 9549
HNISZ DENES ET AL: "Super-Enhancers in the Control of Cell Identity and Disease", CELL, ELSEVIER, AMSTERDAM NL, vol. 155, no. 4, 10 October 2013 (2013-10-10), pages 934 - 947, XP028768422, ISSN: 0092-8674, DOI: 10.1016/J.CELL.2013.09.053 *
HUANG ET AL.: "SOXE Transcription Factors Form Selective Dimers on Non-Compact DNA Motifs through Multifaceted Interactions between Dimerization and High-Mobility Group Domains", SCIENTIFIC REPORTS, vol. 5, 2015, pages 1 - 12
JOLMA ET AL.: "Multiplexed Massively Parallel SELEX for Characterization of Human Transcription Factor Binding Specificities", GENOME RESEARCH, vol. 20, no. 6, 2013, pages 861 - 73, XP055074906, DOI: 10.1101/gr.100552.109
KARLSSONVON HOFSTENOLSSON: "Generating Transparent Zebrafish: A Refined Method to Improve Detection of Gene Expression during Embryonic Development", MARINE BIOTECHNOLOGY, vol. 3, no. 6, 2001, pages 522 - 27
KAWAKAMI: "Tol2: A Versatile Gene Transfer Vector in Vertebrates", GENOME BIOLOGY, vol. 8, 2007, pages 1 - 10
KWAN ET AL.: "The Tol2kit: A Multisite Gateway-Based Construction Kit for Tol2 Transposon Transgenesis Constructs", DEVELOPMENTAL DYNAMICS, vol. 236, no. 11, 2007, pages 3088 - 99, XP008094309, DOI: 10.1002/dvdy.21343
LOPEZ-BERTONI ET AL.: "DNMT-Dependent Suppression of MicroRNA Regulates the Induction of GBM Tumor-Propagating Phenotype by Oct4 and Sox2", ONCOGENE, vol. 34, no. 30, 2015, pages 3994 - 4004, XP036973060, DOI: 10.1038/onc.2014.334
LUJAN ET AL.: "Direct Conversion of Mouse Fibroblasts to Self-Renewing, Tripotent Neural Precursor Cells", PNAS, vol. 109, no. 7, 2012, pages 2527 - 32, XP002679170, DOI: 10.1073/PNAS.1121003109
MACLEOD ET AL.: "Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells", CELL REPORTS, vol. 27, no. 3, 2019, pages 971 - 986
MARTELLA ET AL.: "EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors", ACS SYNTHETIC BIOLOGY, vol. 6, no. 7, 2017, pages 1380 - 92
MCLEAN ET AL.: "GREAT Improves Functional Interpretation of Cis-Regulatory Regions", NATURE BIOTECHNOLOGY, vol. 28, no. 5, pages 495 - 501
MUERDTER ET AL.: "Resolving Systematic Errors in Widely Used Enhancer Activity Assays in Human Cells", NATURE METHODS, vol. 15, no. 2, 2018, pages 141 - 49
NUSSLEIN-VOLHARDDAHM: "Zebrafish: a practical approach", 2002, OXFORD UNIVERSITY PRESS, pages: 303
POLLARD ET AL.: "Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens", CELL STEM CELL, vol. 4, no. 6, 2009, pages 568 - 80, XP002665238, DOI: 10.1016/j.stem.2009.03.014
QUINLANHALL: "BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features", BIOINFORMATICS, vol. 26, no. 6, 2010, pages 841 - 42, XP055307411, DOI: 10.1093/bioinformatics/btq033
S. K. SINGH ET AL.: "Identification of Human Brain Tumour Initiating Cells", NATURE, vol. 432, no. 7015, 2004, pages 396 - 401, XP002467853, DOI: 10.1038/nature03128
SOUFI ET AL.: "Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming", CELL, vol. 161, no. 3, 2015, pages 555 - 68
STOTHARD: "Internet On-Ramp", BIOTECHNIQUES, vol. 28, no. 6, 2000, pages 1102 - 4
STRICKER ET AL.: "Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner", GENES DEV, vol. 27, no. 6, 2013, pages 654 - 69
SUVA ET AL.: "Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells", CELL, vol. 157, no. 3, 2014, pages 580 - 94, XP055579861, DOI: 10.1016/j.cell.2014.02.030
TANG FAQING ET AL: "Abstract", NPJ PRECISION ONCOLOGY, vol. 4, no. 1, 1 December 2020 (2020-12-01), XP055821816, Retrieved from the Internet <URL:https://www.nature.com/articles/s41698-020-0108-z.pdf> DOI: 10.1038/s41698-020-0108-z *
WHYTE WARREN A ET AL: "Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes", CELL, ELSEVIER, AMSTERDAM NL, vol. 153, no. 2, 11 April 2013 (2013-04-11), pages 307 - 319, XP028547941, ISSN: 0092-8674, DOI: 10.1016/J.CELL.2013.03.035 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2024023530A1 (en) * 2022-07-29 2024-02-01 The University Court Of The University Of Edinburgh Functional nucleic acid molecule and method

Also Published As

Publication number Publication date
JP2024504412A (en) 2024-01-31
KR20230137399A (en) 2023-10-04
CN116867901A (en) 2023-10-10
AU2022212766A1 (en) 2023-08-24
WO2022162361A1 (en) 2022-08-04
CA3206298A1 (en) 2022-08-04
US20240092847A1 (en) 2024-03-21
BR112023014906A2 (en) 2023-10-31
EP4284935A1 (en) 2023-12-06
AU2022212766A9 (en) 2024-09-19

Similar Documents

Publication Publication Date Title
Lim et al. Treatment of a mouse model of ALS by in vivo base editing
Zhao et al. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation
US20240092847A1 (en) Functional nucleic acid molecule and method
Tichon et al. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells
Lv et al. lncMGPF is a novel positive regulator of muscle growth and regeneration
EP3494997B1 (en) Inducible dna binding proteins and genome perturbation tools and applications thereof
Ding et al. Tex10 coordinates epigenetic control of super-enhancer activity in pluripotency and reprogramming
Liu et al. Six1 regulates MyoD expression in adult muscle progenitor cells
JP2018505219A (en) Compositions and methods for epigenome editing
CN114555805A (en) Compositions and methods for identifying modulators of cell type fate specialization
JP2023538964A (en) Synthetic miniaturized CRISPR-CAS (CASMINI) system for eukaryotic genome engineering
US20240100185A1 (en) Compositions and methods for the targeting of ptbp1
WO2023051734A1 (en) Engineered crispr-cas13f system and uses thereof
EP3302522B1 (en) Means and methods for treating facioscapulohumeral muscular dystrophy (fshd).
JP2024511621A (en) Novel CRISPR enzymes, methods, systems and their uses
Du et al. NOVA1 promotes SMN2 exon 7 splicing by binding the UCAC motif and increases SMN protein expression
WO2024023530A1 (en) Functional nucleic acid molecule and method
US20240309347A1 (en) Fusion Proteins for CRISPR-based Transcriptional Repression
US20210254161A1 (en) Method for determining decrease in functions of hippocampus by using correlation between micro rna and nmda receptor, method for inhibiting decrease in functions, and method for screening for inhibitors of decrease in functions
WO2023184107A1 (en) Crispr-cas13 system for treating mecp2-associated diseases
Yamamoto et al. Engineering of AAV-Mediated in Vivo Targeted DNA Methylation Editing System via Staphylococcus Aureus Derived Cas9-SunTag
WO2023086026A2 (en) Method and composition for inhibiting telomerase activity
Shah Human neuronal LUHMES cell line as a model system for studying Rett syndrome
Chesnokova et al. Regulatory Elements for Gene Therapy of Epilepsy
CN119343448A (en) Non-LTR retrotransposon subsystem and application thereof

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION HAS BEEN PUBLISHED

AK Designated contracting states

Kind code of ref document: A1

Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20230204